The Eugenics Wars are a backstory event in the fictional Star Trek universe. First mentioned in the TOS episode "Space Seed", in which it was stated that the "Eugenics War" was a global conflict that occurred during the mid to late 1990s. The progeny of a genetic engineering project established themselves as supermen and attempted world domination. The most notable of them, Khan Noonien Singh, conquered a quarter of the planet, mostly Asia. They ended up fighting amongst themselves and were eventaully overthrown due to their disunity. Khan, however, escaped into space with a group of his followers only to be encountered by the USS Enterprise after spending centuries in suspended animation. Much like the Butlerian Jihad in the Dune universe, the Eugenics Wars are the primary reason for many restrictions and prohibitions on genetic manipulation within the Star Trek universe.

At the time "Space Seed" was written, the Eugenics Wars were inferred to be large-scale global conflicts. However, after the very different reality of the actual 1990s, the Eugenics Wars have been retconned in some non-canon Star Trek novels that describe them as much quieter conflicts, secret wars that occurred mostly in the shadows of the major conflicts and events of that decade with Gary Seven and his assistant being Khan's principal opponents. However, the Star Trek: Enterprise episode "Borderland" reaffirmed in canon that 30 million people died in the conflict. In the two-part USS Voyager episode "Future's End", the crew of USS Voyager was transported to Earth in 1996, where it is shown that, at the very least, the Los Angeles region was spared any direct impact of the Eugenics Wars.

In "Space Seed" Mr. Spock refers to the Eugenics Wars being Earth's "third world war". This statement has been quietly ignored, however, and in the Star Trek Universe, World War III is said to have taken place in the mid 21st century, ending in 2053. The use of a plural to describe "Eugenics Wars" has never been officially explained either, suggesting that there was likely more than one conflict within a short period of time (similar to the real world enduring two Gulf Wars in a little over a decade).

Captain Jonathan Archer's great-grandfather was in North Africa during the Eugenics Wars. His battalion was evacuating civilians from a war zone when they came under attack. There was a school full of children directly between them and the enemy. If his men had returned fire, they might have hit it. So he called the commander on the other side and got him to agree to hold his fire long enough to evacuate the school.

An episode of Star Trek: Deep Space Nine ("Dr. Bashir, I Presume") suggested that the Eugenics Wars occurred not in the 1990s, but in the late 21st Century. This was later dismissed as a continuity error on the behalf of the episode writers and not an official retconning of the event.

A three-episode story arc of Star Trek: Enterprise in October and November 2004 examines some of the aftermath of the Eugenics Wars in the years before "Space Seed". At least one media report released prior to the broadcast of the arc's first episode, "Borderland", erroneously stated that the series was going to retcon the Eugenics Wars into happening in the 22nd Century, but this turned out to be a false report.