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- Twelve Ounce Mouse
- Sixteen
- The Adventures of Jimmy Neutron Boy Genius
- Alienators Evolution Continues
- All Grown Up
- Alpha Teens On Machines
- The Amazing Spiez
- American Dad
- American Dragon Jake Long
- Angelina Ballerina
- Animal Mechanicals
- Animalia
- Aqua Teen Hunger Force
- Archer
- As Told by Ginger. Had most of its run in this decade.
- Atomic Betty
- Avatar: The Last Airbender
- Baby Looney Tunes
- Back at the Barnyard
- The Backyardigans
- The Batman
- Batman Beyond (although it began in 1999)
- Batman: Mystery of the Batwoman
- Batman the Brave And The Bold
- Ben 10
- Biker Mice From Mars (the 2006 Revival)
- Da Boom Crew
- The Boondocks
- Bounty Hamster
- Braceface
- Bradys Beasts
- The Brak Show
- Brandy and Mr. Whiskers
- Bratz. Based on the toyline.
- The Bremen Avenue Experience
- Bromwell High
- Bro Town
- Butt Ugly Martians
- Buzz Lightyear of Star Command
- The Buzz on Maggie
- Camp Lazlo
- Captain Flamingo
- Carl Squared
- Casper Scare School
- Catscratch
- Chalk Zone
- Chaotic
- Charlie and Lola. Adaptation of the book series.
- Chop Socky Chooks
- Chowder
- Chuggington
- Class of 3000
- Class of the Titans
- Clerks
- The Cleveland Show
- Clone High
- Coconut Freds Fruit Salad Island
- Code Lyoko
- Code Monkeys. Set in The Eighties.
- Codename: Kids Next Door
- Combo Ninos
- The Cramp Twins.
- Curious George. Adaptation of the book series.
- Cyberchase
- Danny Phantom
- The Dating Guy
- Dave the Barbarian
- Delgo
- Delilah and Julius
- Di-Gata Defenders
- Dino Squad
- Dinosaur Train
- Doodlez
- Dora the Explorer
- Dragon Booster
- Drawn Together
- The Drinky Crow Show
- Duck Dodgers
- Eckhart
- Edgar and Ellen. Animated adaptation of the literary series.
- El Tigre
- The Emperors New School
- Evil Con Carne
- The Fairly Odd Parents: Started as a series of cartoon shorts in 1998, but became a regular series in 2001 and it really came into its own in 2001-2003, of course Your Mileage May Vary concerning later episodes.
- Family Guy (started in 1999, cancelled in 2002, Un Cancelled in 2005)
- Fanboy and Chum Chum
- Fantastic Four Worlds Greatest Heroes
- Fatherhood
- Father of the Pride
- Fifi and the Flowertots
- Fillmore
- Flushed Away
- Foot 2 Rue
- Fosters Home for Imaginary Friends
- Frannys Feet
- Freak Show
- Freds Head
- Frisky Dingo
- Futurama (debuted in 1999, but gained most of its following during its 2003-2007 hiatus)
- The Future Is Wild
- Gadget and the Gadgetinis
- The Garfield Show
- Gary the Rat
- George of the Jungle. Second series.
- Geronimo Stilton (the books' Animated Adaptation debuted in 2009)
- Get Ed
- G.I. Joe
- Glenn Martin DDS
- Go Diego Go
- God the Devil And Bob
- Gormiti the Lords of Nature Return
- The Grim Adventures of Billy and Mandy
- Grossology
- Growing Up Creepie
- Handy Manny
- Harvey Birdman Attorney At Law
- Hot Wheels Battle Force 5
- House of Mouse
- Iggy Arbuckle
- Invader Zim
- Iron Man Armored Adventures
- Jackie Chan Adventures
- Jacob Two Two
- Jakers the Adventures of Piggley Winks
- Jimmy Two Shoes
- Johnny Test
- Jungle Junction
- Justice League
- Kappa Mikey
- Kenny the Shark
- Kid VS Kat
- Kim Possible
- King Arthurs Disasters
- Kong the Animated Series
- Korgoth of Barbaria
- Krypto the Superdog
- League of Super Evil
- The Legend of Tarzan
- Legion of Super Heroes
- The Life and Times of Juniper Lee
- Lilo and Stitch The Series
- Little Einsteins
- Lloyd in Space
- Lola and Virginia
- Loonatics Unleashed
- Magi Nation
- Making Fiends
- Mama Mirabelles Home Movies
- Martha Speaks
- Martin Mystery
- The Marvelous Misadventures of Flapjack
- Max and Ruby
- Max Steel
- Maya and Miguel
- Megas XLR
- Metalocalypse
- Mickey Mouse Clubhouse
- The Mighty B
- Miss Spiders Sunny Patch Friends
- Mr. Meaty
- The Mr. Men Show
- Monkey Dust
- Monster Allergy. Adaptation of the comic book series.
- Monster Buster Club
- Moral Orel
- Mucha Lucha
- My Dad the Rock Star
- My Gym Partners a Monkey
- My Life as a Teenage Robot
- My Little Pony
- Ni Hao Kai Lan
- Oban Star Racers
- The Oblongs
- O'Grady
- Olivia
- Ozzy and Drix
- Peep and the Big Wide World
- Pelswick
- The Penguins of Madagascar
- Peppa Pig
- Perfect Hair Forever
- Pet Alien
- Phineas and Ferb
- Pocoyo
- Potatoes and Dragons
- The Proud Family
- The Replacements
- Rick and Steve
- Ricky Sprocket Showbiz Boy
- The Ripping Friends
- Roary the Racing Car
- Robotboy
- Robot Chicken
- Rotting Hills
- Ruby Gloom
- Sagwa the Chinese Siamese Cat
- Samurai Jack
- Scooby Doo
- Sealab 2021
- Sea Princesses
- The Secret Saturdays
- The Secret Show
- Shaolin Wuzang
- Shaun the Sheep
- Sheep in The Big City
- Shuriken School
- Sid the Science Kid
- Silverwing: Adaptation of the novels.
- Simplemente Rita
- Sit Down Shut Up
- Sitting Ducks
- Skunk Fu
- Skyland
- Slacker Cats
- Sons of Butcher
- Special Agent Oso
- The Spectacular Spider Man
- Speed Racer the Next Generation
- Spider Man the New Animated Series
- Spliced
- Squidbillies
- Squirrel Boy
- Stanley
- Stargate Infinity
- Star Wars Expanded Universe
- Star Wars Clone Wars (2003)
- Star Wars the Clone Wars (2008)
- Static Shock
- Stoked
- Storm Hawks
- Strawberry Shortcake. First television series.
- Stripperella
- Super Why
- The Superhero Squad Show
- Tak and the Power of Juju
- Team Galaxy
- Teamo Supremo
- Teen Titans
- Teenage Mutant Ninja Turtles
- Three Delivery
- Time Squad
- Time Warp Trio
- Timmy Time
- Titan Maximum
- Total Drama Island
- Totally Spies
- Transformers
- Tripping the Rift
- Trollz
- Tupu
- Tutenstein
- Ultimate Book of Spells
- The Venture Brothers
- Viva Pinata
- Wakfu
- Watch My Chops
- Wayside
- The Weekenders
- Whatever Happened to Robot Jones
- Will and Dewitt
- Winx Club
- WITCH
- Wolverine and the X-Men
- Word Girl
- Word World
- World of Quest
- Wow Wow Wubbzy
- The Xs
- Xiaolin Showdown
- X-Men Evolution
- Yakkity Yak
- Yin Yang Yo
- The Zeta Project