Andronesian Encephalitis
An unpleasant, but not life-threatening, disease transmitted by airborne particles that is common in Federation space due to the transmission of the particles via space travel.  The disease was easily treated and was regarded as a minor condition in 2365.  TNG "The Dauphin"

Aphasia Virus
An artificial virus created by the Bajoran underground in 2351 during the Cardassian hostilities, which spread throughout Deep Space Nine.  Intended to be used against the Cardassian occupiers, the device carrying the virus lay dormant until 2369, when it accidentally infected Bajoran and Federation personnel, leaving each sufferer unable to communicate in a coherent manner.  Aphasia was only the initial symptom, and as the sickness progressed the sufferer eventually slipped into a coma and died.  DS9 "Babel"

Arethian Flu
A common viral disease.  On Stardate 48579, the U.S.S. Voyager NCC-74656's Emergency Medical Hologram suspected that Lt. Hargrove might have Arethian flu.  VOY "Eye of the Needle"

Ba'ltmasor Syndrome
A degenerative disease that is endemic to the Klingon species.  The condition is treatable with a course of regualr injections, which prevents the symptoms from escalating.  TNG "The Drumhead"

Barclay's Protomorphosis Syndrome
An intron virus that caused numerous humanoid, and several animal, species to experience structural and behavioral changes characteristic of forms from earlier stages in their evolutionary development.  Accidentally developed when a routine synthetic T-cell treatment became mutated, the virus worked by invading the host's DNA, and activating introns - the portions of an individual's genetic code that are normally dormant, and which contain holdovers from previous evolutionary stages.  Named for the U.S.S. Enterprise NCC-1701-D's Lt. Reginald Barclay, the first individual known to contract the virus, Barlcay's Protomorphosis Syndrome came close to incapacitating the entire crew of the Enterprise in 2370.  TNG "Genesis"

Bendii Syndrome
A degenerative illness affecting a minority of elderly Vulcans.  Initially it is characterized by a gradual but accelerating loss of emotional control, with victims exhibiting sudden bursts of emotion.  Diagnosis is made by culturing a tissue sample taken from the patient's metathalamus.  A dangerous side effect of Bendii Syndrome is that the loss of emotional control can be telepathically projected to others.  Vulcans are able to resist the emotional projections, but if the afflicted person is in the presence of non-Vulcans the emotions can cause outbreaks of Violence.  Ambassador Sarek was afflicted with Bendii Syndrome at the age of 202, and his struggle with the condition ended in 2368, when he died.  TNG "Sarek"

Blood Fever
A neurochemical imbalance caused by the Vulcan Pon farr mating drive.  The Vulcan telepathic mating bond, particularly if used on a non-Vulcan, caused potentially fatal hormonal changes, which have devastating physiological effects.  The only two outlets that alleviate the blood fever are those offered by the ancient Koon-ut-kal-if-fee - marriage or challenge - ritual.  The victim must either complete the mating bond, or engage in potentially lethal combat.  VOY "Blood Fever"

Chromo-Viral Disease
A chromo-viral disease is easily transmitted and passes through several increasingly critical stages; it can be treated successfully with cytoglobin injections.  VOY "Critical Care"

Dermal Dysplasia
A skin disorder caused by an overexposure of the victim's epidermis to hazardous levels of thermal and ultraviolet radiation, usually from the local sun.  VOY "Future's End, part I"

Dorek Syndrome
A rare and untreatable terminal disease that afflicts one out of every five million Ferengi.  By the time it is diagnosed, the sufferer has on average only six or seven days to live, although they do retain their full capabilities until the last moments of the disease's progress.  DS9 "Body Parts"

Hemocythemia
A medical condition which results in the intercellular pressures of its host becoming unstable.  The illness was also referred to as hemocytemic imbalance.  There is a prescribed treatment for the condition, which is effective in all but the very extreme cases, and that is through the application of osmotic pressure therapy.  VOY "Deadlock"

Holotransference Dementia Syndrome
A psychological disturbance in which an individual becomes so disoriented within a holographic scenario that they lose sense of their own true identity and start to believe that they are part of the program.  VOY "Projections"

Hesperan Thumping Cough
A flu-like affliction contracted via an airborne virus, one symptom of which is severe respiratory distress.  This illness resembles the whooping cough of 20th-century Earth, and is marked by a convulsive spasmodic cough.

Iresine Syndrome
A very rare neurological disorder in humanoids, characterized by a peculiar electropathic signature in the thalamus and a severely decreased histamine count; sufferers fall into a coma of duration of approximately 72 hours.  This disorder was first identified in the 23rd century.  TNG "Violations"

Irumodic Syndrome
Degenerative neurological disorder that causes deterioration of the synaptic pathways.  The condition causes confusion, delusions, and eventually death.  The treatment of choice in 2370 was peridaxon, through this only relieved the symptoms.  Genetic testing determines if a person may develop Irumodic Syndrome in later life, but not all persons who test positive develop the condition.  TNG "All Good Things..."

Iverson's Disease
A chronic and progressive muscular disorder that cuases fatal degeneration of motor skills in humans, but does not impair mental faculties.  There is no known cure for this disease.  TNG "Too Short a Season"

Kalla-Nohra Syndrome
A chronic pulmonary disease with a unique pathology.  This syndrome is only found among survivors of a mining accident at Gallitep, a forced labor camp run by the Cardassians during their occupation of Bajor.  All known survivors of Gallitep have the syndrome, and there are no recorded instances of anyone being diagnosed with the disease unless they were at the camp.  Palliative medication is effective in alleviating the symptoms.  The condition is similar to the less-damaging Pottrik Syndrome; an effective differential diagnosis between the two conditions is a lower respiratory probe, which gives a positive result for Kalla-Nohra.  DS9 "Duet"

Levodian Flu
A minor viral disease which lasts 29 hours.  Symptoms include a runny nose and persistent sneezing.  Levodian flu is generally regarded as an annoyance rather then a medical emergency.  VOY "Tattoo"

Mendakan Pox
A disease in humanoids characterized by an otherwise harmless skin mottling.  VOY "Favorite Son"

Memory Virus
A parasitic organism, possessed of some degree of intelligence, that survives on the peptides generated by its host's brain.  The virus evades the body's immune system by disguising itself as a memory engram, creating a false memory for its host that is so traumatic that the host's psyche represses it.  In host after host, the virus survives by hiding in a part of the host's mind that the subconscious  would want to avoid at all costs.  When it senses the death of the host, it implants itself in another victim.  Thoron radiation proves fatal to this organism.  VOY "Flashback"

Morphogenic Virus
An artificially-generated virus created by the covert Federation organization Section 31 to inhibit the Founders from changing shape during the latter part of the Dominion war in 2375.  DS9 "When it Rains"

The Nehret
The Nehret is a virus that lies dormant, disgusing itself as inert genetic material until it inexplicably actives.  In 2377 the Nehret was eradicated using stem cells from the mixed-heritage baby belonging to Lt. Tom Paris and B'Elanna Torres.

Orkett's Disease
A viral malady that swept through the Bajoran work camps during the Cardassian occupation, killing thousands of Bajoran children.  VOY "State of Flux"

Phage
Without a doubt, one of the most virulent contagions discovered by Federation personnel was the phase; a deadly virus that attacked members of the Vidiian race in the Delta Quadrant.  The phage literally consumed the Vidiians; their genetic code was first disrupted, then their body tissues were consumed.  One of the early symptoms of the disease was excruciating joint pain.  Some victims had been known to die simply from the agony itself, and euthanasia of afflicted persons was common.  The Vidiians survived in the short term by making extensive use of transplantation and organ piracy, using a variant of transporter technology to literally steal healthy organs from the bodies of their owners.  Increasingly desperate, the Vidiians resorted to kidnapping members of other species and experimenting on them.  A Vidiian scientist, Sulan, believed that research into Klingon genetic material would eventually lead to a cure.  Whether this line of investigation would have been successful became moot when it was revealed that the coalition known as the "think tank" had devised a cure for the phage.  Now cured of the disease that had been ravaging their society for so long, the Vidiians had to face the consequences of the actions they took in their desperate struggle, which cost the lives of so many innocents.  VOY "Phage"

Phyrox Plague
A particularly virulent disease that swept the planet Cor Caroli V in 2366.  Starfleet Command classified the outbreak as secret after intervention by the U.S.S. Enterprise NCC-1701-D contained the virus.  TNG "Allegiance"

Plasma Plague
A family of lethal virus types, one of which threatened the heavily populated Rachelis system in 2365.  The plsma plaque viruses were known for almost a century prior to 2365, and pioneering research was conducted by Dr. Susan Nuress in 2295 following an epidemic on planet Obi VI.  One mutated strain, developed during Nuress's explorations, was discovered to grow more rapidly when exposed to eichner radiation.  A smiliar strain threatened the U.S.S. Enterprise NCC-1701-D, when the ship was transporting speciems of plsma plaque to science station Tango Sierra to combat the Rachelis system contagion.  TNG "The Child"

Pottrik Syndrome
A disorder similar to Kalla-Nohra Syndrome that is treated using the same medication.  A bio-probe can be used to distinguish between the similar conditions.  DS9 "Duet"

Psi 2000 Virus
A water-based organism originally found on planet Psi 2000 in 2266.  The virus infected members of the Federation science team stationed on that planet, causing them to exhibit irrational behavior that eventually led to their deaths.  Transmitted through contact in humanoid perspiration, the virus later affected the members of the U.S.S. Enterprise NCC-1701 crew, resulting in the near-destruction of the ship.  An antidote was found, but a similiar virus that was carried by airborne particles infected members of the U.S.S. Tsiolkovsky NCC-53911 and the U.S.S. Enterprise NCC-1701-D in 2364.  TOS "The Naked Time," TNG "The Naked Now"

Rigelian Fever
A lethal disease resembling the bubonic plague - as seen on Earth - in its effects.  The only known antidote, ryetalyn, is extremely rare and difficult to chemically synthesize.  TOS "Requiem for Methuselah"

Radiation Disease
Radiation disease was initially caused by the unwitting tampering of an antimatter reactor core on a Delta Quadrant world; a nuclear winter that lasted decades ensued.  Sufferers endured horrific skin complaints as a result of exposure to the radiation, but all conditions were treatable.  VOY "Friendship One"

Rigelian Kassaba Fever
A disease treated with stokaline injections, presumably less virulent than standard Rigelian fever.  TOS "By Any Other Name"

Rudellian Brain Fever
A cerebral infection prevalent on Bajor and in other worlds formerly administered by Cardassia.  DS9 "The Assignment"

Rop'ngor
A juvenile Klingon disease that results in skin eruptions and malaise similar in effect to Terran measles.  Very rarely seen in adult Klingons, unless they are in poor physical condition, and considered a very embarrassing affliction in adulthood.  TNG "Up the Long Ladder"

Rugalan Fever
A deadly disease prevalent on the Trill homeworld.  Those who survive the illness are severely incapacitated for a number of weeks.  DS9 "Nor the Battle to the Strong"

Rudellian Plague
A virulent illness that swept through a Cardassian colony on the planet Pentath III in 2372.  DS9 "Rules of Engagement"

Rushton Infection
A lethal disease that was still prevalent, and sudden in its effects, in 2361.  TNG "The Bonding"

Sakuro's Disease
A extremely rare but dangerous condition that can cause fever, weakness, and, ultimately, death if left untreated.  TOS "Metamorphosis"

Symalene Blood Burn
A virulent contagion that could, if unchecked, kill an entire planetary population within an extremely short space of time.  TOS "The Changeling"

Synthococcus Novae
A dangerous, but treatable contagion, which was a bacillus-strain side effect of modern technology.  It was regarded as a serious health hazard, with suffers being required to notify their status to the authorities.  Rare individuals carry the disease in dormant form, infecting others while being immune themselves.  

Tarkalean Flu
Takalean flu is a non-life-threatening ailment that is manifested with fever, respiratory distress, and tremors, but lasts only a few days.  VOY "Body and Soul"

Tellurian Plague
A virulent and lethal infection that was still prevalent and incurable, in the 2360's.  TNG "A Matter of Time"

Terellian Death Syndrome
An extremely unpleasant condition relating to cellular decay, which, despite its sinister name, can easily be reversed if diagnosed early enough.  Symptoms include dizziness, blurred vision, cardiac palpitations, and a stinging sensation in the lower spine.  TNG "Genesis"

Teplan Blight
A viral disease endemic to the population of a planet located in the Teplan system.  The disease was brought to the planet by the Jem'Hadar as punishment for not accepting Dominion control.  The blight was congenital, present in each individual at birth and characterized by lesions that are blue at birth, but redden upon death.  In 2372, the Starfleet physician Dr. Julian Bashir, though unable to cure the mature form of the disease, was able to devise a vaccine that eradicated the blight from unborn children, insuring future generations were disease-free.  DS9 "The Quickening"

Terrellian Plague
A particularly virulent disease which, in the anti-time universe created by Q, became virtually out of control in 2395.  Following an outbreak on Romulus, the Klingon Empire allowed medical ships to cross the border of the Neutral Zone to offer aid.  TNG "All Good Things..."

Terra Nova Radiation Sickness
The inhabitants of mankind's first deep space colony, Terra Nova, were subjected to lethal forms of radiation after an asteroid ploughed into their planet.  The resulting shockwave from the impact formed a radioactive cloud that poisoned the atmosphere of the northern hemisphere for 70 years.  The Novans fled underground, but suffered from radiation sickness, and various cancers soon became prevalent.  The Novans had to abandon their subterranean homes Novans had to abandon their subterranean homes when a bersium isotope contaminant entered the ground water supply and caused them to suffer from micro-cellular decay.  The Novans were relocated to the southern hemisphere, where they were finally safe from the effects of the "poison rain."  ENT "Terra Nova"

Thelusian Flu
A virus causing minor respiratory distress, endured by the first officer of the U.S.S. Lantree NCC-1837.  TNG "Unnatural Selection"

Tetracyanate Poisoning
In 2151 the inhabitants of an Akaali city were being poisoned by a covert and illegal mining operation for veridium isotopes.  An industrial lubricant, Tetracyanate 622, which was used in the mining process, had leaked into the area's water supply, consequently infecting the local population.  The isotope caused lesions and mottled the skin of the infected, and if not treated usually proved fatal.  ENT "Civilization"

Transporter Psychosis
This rare medical disorder was caused by a breakdown of neurochemical molecules during transport, affecting the body's motor functions as well as the autonomic systems and the higher brain functions.  Frequent early symptoms were sleeplessness, tachycardia, muscular spasms, myopia, and dehydration.  More acute cases manifested paranoia, hallucinations, delusions, and psychogenic hysteria, and, in extreme cases, multi-infarct dementia caused by dead zones in the cerebral tissues.  First diagnosed in 2209 by researchers on Delinia II, the problem resulted from an imperfect understanding of the effects of transporter technology on humanoid physiology, and was eliminated in 2319 with development of the multiplex pattern buffer.  TNG "Realm of Fear"

Tropolisine-Induced Psychosis
Ab exploratory landing party sent from the Enterprise NX-01 to a Minshara-class world was exposed to a pollen, which contained a psychotropic agent named Tropolisine.  Those infected suffered anxiety and paranoia, and were subject to intense hallucinations.  Dr. Phlox's analysis of the compound revealed that it contained a stray neutron, which, when broken down, released a toxin that could prove fatal if not treated with inaprovaline.  Ensign Novakovich was almost killed after his exposure to the alien pollen.  ENT "Strange New World"

Almost complete with this listing.