Leonardo - "Leo" is a hardworking ninjutsu student, learning how to be an effective leader for his three often unruly brothers. He wears a blue mask and fights with two katana swords called Niten Ryu.
Donatello - "Donnie" is in charge of the design and manufacture of all of the tools and weapons in the Turtles' arsenal, and he is also a gifted hacker. He wears a purple mask and fights with a rokushakubo which converts to a naginata. He has a crush on April in this series and his brothers tease him about it.
Raphael- "Raph" often lets his impulsiveness get in the way of rational thinking. He wears a red mask and fights with two sai.
Michelangelo - "Mikey" loves video games, skateboarding, pranks and pizza. He wears an orange mask and fights with two nunchaku, which convert into kusarigama. Though he possesses a child-like innocence, Mikey always brings his best game to a fight.
April O'Neil - The 16 year-old granddaughter of Professor Hector O'Neil who likes to play video games and eat pizza.
Splinter - Splinter is the mutant rat leader of the entire family, and serves as a father figure for the Turtles. He once was a pet for a renowned martial artist, Hamato Yoshi in Japan. It was from watching Yoshi that Splinter first learned the art of ninjitsu which he then passes on to the Turtles. Splinter often acts as much as a spiritual guide and counselor to the team as he does their teacher. While he does not wield a traditional Japanese weapon, Splinter carries a cane which he can utilize as a weapon (like a bo staff) with fierce proficiency. Unlike the previous animated series, the Turtles often refer to Splinter as their father, rather than their master.
Foot Clan - A ninja organization that is led by the Shredder.
The Shredder- One of the primary antagonists of the series and leader of the Foot Clan and former guardian of the Utroms.
Dragonfrill- Chuck Horris is an Australian biker and famous martial artist and secretly a member of the Foot Clan. He is ordered to New York with Borace to find Splinter. As Horris was previously bitten by the frilled lizard, the mutagen transforms him into Dragonfrill, a dragon-like mutant with large frills for ears, and razor sharp teeth.
Rhinohorn - Borace is a street thug until Shredder brought into the Foot Clan. Shredder orders Borace to assist Chuck Horris in finding Splinter. As Borace was previously injured by a black rhinoceros, the mutagen transforms him into Rhinohorn, a spike-backed rhino-like mutant with a large arms, acute senses, and super-strength.
Foot Ninjas - The foot soldiers of the Foot Clan.
Foot Troops - The Foot Troops are robotic troops created by Baxter Stockman for the Foot Clan.
The Krain - One of the main antagonists of the series. The Krain are a race of brain-shaped aliens that pilot robotic bodies and who are responsible for bringing mutagen to Earth. The Krain have mastered English and communicate in redundant speech. They are the worst enemies of the Utroms.
Ku'rell - The most ruthless and corrupt leader and conqueror of the Krain the universe has known. Ku'rell dreams of galactic domination, and wants vengeance against the Utroms for imprisoning him and denying him his dreams by building an army and attacking their homeworld.
Baxter Stockman - Baxter Stockman is an inventor who plotted revenge against a company called TCRI, after he was fired for spilling copier toner.
Triceratons - They are a warring alien race with the appearance of a humanoid triceratops that the Turtles come into contact with when they are accidentally transported across several galaxies at the end of the first season while attempting to find the missing Master Splinter. The Turtles then become a public enemy of the Triceratons for harboring a fugitive known as the Fugitoid, who possesses a transporting technology that the Triceratons desperately want. The Triceratons wish to use Professor Honeycutt's technology to aid them in their war with the Krain. Later in the series, the Triceratons invade earth believing that the Fugitoid is still in hiding there when in reality he has gone to live with the Utrom on their homeworld.
Bearfang - Fang is a Russian thug working for the Krain as their gateway driver. The Turtles interrogate him and find out where the Krain are holding April and Hector O'Neil. During their mission to rescue the O'Neils, the Turtles crash a truck full of mutagen into the Krain base. Fang is exposed to the the mutagen and scratched by a grizzly bear which turns him into a hunchbacked, bear-like mutant with a large hands that Michelangelo dubs "Bearfang". The Turtles fight Bearfang. Leonardo lures him into a sewers where Bearfang falls down. After the Turtles leave, Bearfang is now furious that he has been transformed into a giant bear, the one thing he hates most in the world, even more than the Shredder. Consumed with hatred, he joins the Shredder to help him destroy the Turtles.
Mutagen Man - Seymour is a Cuban thug who videotaped the Turtles on his cellphone during a rooftop battle with the Krain after one of the Turtles knocked out his satellite dish. When Seymour attempts to sell his video to the Krain, he joins them. The Turtles interrogate him and find out where the Krain are kidnapping April. During their mission to rescue April, Seymour fell in a vat of mutagen and turned into a large, bio-mechanical monster (with a body resembling a pile filled with guts and organs, a muscular human arms, and a robot legs) who Michelangelo dubs "Mutagen Man". Besides using ooze attacks, Mutagen Man can also shoot a green, acid-like substance from his belly. Mutagen Man blames the Turtles for his mutation. After a fight with the Turtles in which they broke his cellphone, Mutagen Man vowed revenge and fled.
Dr. Hector O'Neil - A scientist who is April O'Neil's grandfather. He and April were captured by the Krain. Although April was rescued by the Turtles, the Krain made off with Kirby.
Utroms - Utroms are the peaceful aliens who resemble a brain.
Mr. Mortu - Mortu was the captain of the Utrom ship that crashed on Earth. After the crash, he remained the field-leader of the marooned Utroms, and worked as their liaison to the Humans. In the modern day, this makes him CEO of the front company TCRI. His name is "Utrom" backwards.
Dr. Xeinos - She was a beautiful, Utrom scientist who found and raised Leatherhead as her son.
Leatherhead - Leatherhead is an alligator that was originally owned by a young boy until he died in a car accident and Leatherhead fall into a storm drain, where he was found by Dr. Xeinos and other Utroms when they discovered that their mutagen (the same that transformed the Turtles) made him sentient. Leatherhead lived with the Utroms peacefully until the Krain took him to their ship and experimented on him. Leatherhead eventually escapes from the Krain.
Angelica Flowerson- A 16-year-old, bespectacled, beautiful girl who is April's cousin and Leonardo's love interest, sweatheart, and girlfriend. She mostly wears a pink shirt with a white skirt, and gray hi-tops. Angelica befriends the Turtles after the Krain kidnap her. After the Krain took her, they turned her into a white, cat-like mutant, and experimented on her. She is considered a slight damsel-in-distress, as she has been kidnapped by the enemies She truly belongs with Leo as his true love.
Pebble - A penguin that was mutated by the Krain. Pebble learned to talk and befriended April and the Turtles.
Zog - One of the Triceraton soldiers left on Earth when the Utroms left. Some time later, Raphael found him in the sewers, and the Turtles used him to aid in their attack on the Krain.