| Character | Voice Actor | Notes |
|---|
| Agent J | Keith Diamond | Agent J (originally James Darrel Edwards III) is one of the main agents of the organization. He is energetic, and tries to bring emotion back to the bland organization. At one point, J arrests the alien Jarra for attempting to steal the Earth's ozone layer and sell it on the Black Market. He remains somewhat of a sidekick to Agent K. He is referred as "Slick" by Agent K. Throughout the series, most of the other agents treat J like a total screw-up who never should have been allowed in the MIB. |
| Agent K | Ed O'Ross in Season 1, Gregg Berger in Seasons 2–4 | Agent K (originally Kevin Brown) is a top agent and a founder of the organization; and after working at the organisation for nearly 40 years, he shows nearly no emotion. He and J must constantly fight off his old partner Alpha. |
| Agent L | Jennifer Lien in Seasons 1–3, Jennifer Martin in Season 4 | Agent L (originally Dr. Laurel Weaver) is a morgue worker who joins the MiB after she helps Agent K and J stop Edgar the Bug from stealing The Galaxy. She stays in the medical section of the organization until Season 4, wherein she becomes a field agent with Agent X as her partner. |
| Chief Zed | Charles Napier | The head of the organization and K and J's boss. He is usually shown in his office, high above the main floor of the headquarters. It is known that he took the job of director at some point prior to the incident with Serlena and the Light of Zartha in 1978. |
| Agent D | John Mariano | Agent D (originally Derrick Cunningham) is Agent K's former partner who is now retired after getting too old in the fight against the evil aliens. He was a founding member of the organization. Derrick is seen enjoying his retirement with his wife, before he is wiped out of existence by a time traveling alien-hating bigot, and restored by Agent K and a Cerebro-Enhanced Agent J. |
| Jack Jeebs | Tony Shalhoub in Season 1, Billy West in Seasons 2–4 | Jack Jeebs is a humanoid alien who runs a pawn shop, carrying both alien and human merchandise. Jeebs' head is frequently blasted off, but it grows back within seconds, due to the fact that his race regenerates in oxygen rich environments (and it is rumored his race may be immortal from that same talent). |
| Edgar Bug | N/A; originally portrayed by Vincent D'Onofrio in the film | The main antagonist of the feature film who was killed by Agent L. His only appearance in the series was in a flashback to his death in "The Big Bad Bug Syndrome". Edgar is revealed to have a twin brother named Edwin as well as being the Queen Bug's favorite. His death causes The Queen to put a bounty on L’s head. |
| Edwin Bug | Vincent D'Onofrio | The twin brother of Edgar the Bug who is sent by the Bug Queen to get revenge on Agent L for killing Edgar, and killed by the Worm Guys. |
| Geen | Vincent D'Onofrio | A Bug with a perpetually voracious appetite which landed him M.I.B intergalactic prison. Geen and several other inmates were temporarily released by Doctor Lupo and proceeded to wreak havoc upon the MIB HQ until they were rounded up by K and J. |
| Queen Bug | Mary Kay Bergman | The queen of Edwin and Edgar's planet and mother of all bugs. The Queen Bug put a bounty on Agent L's head, offering royal jelly to the Bug that brings her Elle. She later attempted to colonize Manhattan with a new generation of offspring but was foiled by the MIB. The Queen Bug subsequently attempted to conquer Earth once more but was foiled by Agent K and Agent J who flooded the tunnel which the Bugs were using as a base. She was ultimately vanquished by the combined efforts of K and a temporarily amnesiac J. |
| Frank the Pug | Eddie Barth | Frank the Pug is an extraterrestrial living in New York City, in the guise of a pug. It is later revealed that the "human" at Frank's newspaper stand is a robot, and that Frank's true form still resembles a pug, albeit with a dark green color, antennas, and a 3-pointed tail. |
| The Worm Guys | Patrick Pinney and Pat Fraley | Four aliens that love to drink coffee and relax in the organization's break room. They are renowned for knowing many figures of speech and the organization rulebook. They occasionally help K or J. In the alternate future, the worms are shown as the dominant race after they got slimed and multiplied. |
| Arquillians | N/A | The Arquillians are a race of tiny humanoid aliens. Arquillians have large heads and eyes, but a small body, and hide in human-like robots. The Arquillians are the possessors of the Arquillian Galaxy (a miniaturized 'source of sub-atomic power') and will not stand for it being lost or stolen. They are ruled by a complex monarchy. |
| Baltians | N/A | The first race of aliens encountered by the original agents of the organization: a tall, slender species that vaguely resemble Grey aliens. The Baltians return to Earth every ten years to provide new alien technologies to help fund the organisation. |
| Idikiukup and Bob | Patrick Pinney and Pat Fraley | A pair of alien twins (earning them the nickname of the Twins) that serve as the MIB's head scientists along with Agent L. They mostly stay at headquarters though Bob pilots a helicopter in "It's a Fmall Fmall World". |
| Alpha | David Warner | Alpha is Agent K's former mentor, and now the sworn enemy of the M.I.B. and Agent K. Stealing a Verulian Cosmic Integrator, he used it to graft stolen alien body parts onto himself until he was defeated and captured. Escaping and allying himself with Vangus and the Ixions, Alpha turned himself into a cyborg. Alpha is killed in "Endgame Part 2". J often mockingly calls him "Alfalfa". He is the main antagonist of the series. |
| Buzzard | Sherman Howard | A Zombarian bounty hunter who is an occasional adversary of Agents J and K. Howard and D'Onofrio both previously were guests on Miami Vice and were enemies of Crockett and Tubbs like they were Agent J and K. |
| Dak Jeebs | Billy West | Jack Jeebs' twin brother. |
| Drekk | Ron Perlman | Drekk is alien who has a long criminal record: "longer than Van Allen's belt", according to Chief Zed. He is a former cell-mate of Frank the Pug, and an antagonist of the lead characters. |
| The Emperor Worm | Vincent D'Onofrio | The Emperor Worm is the leader of the Worms. Unlike the other Worms, the Emperor is hugely fat, and almost double the height of the others. He usually shows up un-announced at the organisation. The Emperor is careless and defenseless, so the other Worms must watch him. |
| Agent H | Kurtwood Smith | One of the founding members of the Men-In Black. He was responsible for most of the MIB's medical equipment. |
| Agent Q | N/A | One of the founding members of the organization; responsible for the weapons and vehicles that the organization use. When Q was erased from history, all the weapons and vehicles he developed were erased (and restored) with him. |
| Aileen | Beth Broderick | A female alien and agent of the Men in Black: a blue-skinned humanoid, with malleable hands. She lost her former partner to an alien shapeshifter called an Inanimate. She is later assigned another partner named Eidi, whom she treats similarly to K's treatment of J. Like K, she is a legendary agent on her home planet. |
| Eidi | N/A | Aileen's rookie partner, assigned to her after the capture of the Inanimate. She is the same species as Aileen, but taller and slightly bulkier. Eidi and J bond while working the case due to their shared status as novices partnered with the planet's best agents. |
| Agent U | N/A | An average agent. His name before joining the organization was Upton, which J easily deduces. There is a running gag where U's agent codename and the word "you" are often confused. Agent U is shown to be a major suck up and simply teaches alien children how to disguise themselves as humans though in "The Buzzard Syndrome" Agent U is seen catching a Micrelian criminal. |
| Agent E | N/A | An average agent who also worked in Hollywood, getting work for aliens in movies and television shows. Most of her clients resemble aliens like the Xenomorph and Alf. |
| Agent X | Adam Baldwin | A big-eared, green-skinned alien originating from the G-Dan galaxy; recruited into the organization as Elle's partner, to smooth over human-alien relations. Though he has an impeccable record, X was suspended six times in his home galaxy. |
| Dr. Zan'dozz Zeeltor | Steve Kehela | A blue-skinned humanoid alien who replaces Elle as chief scientific officer of the organization. He is very eccentric about the simple items around Earth. Most of his inventions usually cause more harm around J, such as a sticky note pad that started to constrict him. Zeeltor has a pet named Lucy: a Futavian colony bacterium that makes a roaring sound. |
| Troy The Symbiote | Rino Romano | A young adventurous symbiote who has a playful relationship with J. His dream is to work for the organization, much to his mother's distress. Troy becomes an MIB intern in "The Heads You Lose Syndrome". |
| Klah'Mikk | N/A | A paperwork filing alien who works for the organisation. |
| The Fmeks | N/A | The warmongering counterparts of the Arquillians. The Fmeks are the Arquillian's sworn enemy because the Arquillian's planet is bigger than their home world Fmoo. |
| The Ixions | N/A | A race of oil-loving creatures, who with the help of their leader, Vangus, attempt to plunder the Earth's oil to sell it on the intergalactic market. They were ultimately defeated by MIB, along with Alpha. |
| Vangus | Billy West | The leader of the Ixions. |
