* See article AnimeOfThe2000s.
* ''Anime/AgathaChristiesGreatDetectivesPoirotAndMarple''
* ''Manga/AirGear''
* ''Manga/{{ARIA}}''
* ''Webcomic/AxisPowersHetalia''
* ''Manga/AyashiNoCeres'' (although the manga was made in 1996)
* ''Manga/AzumangaDaioh'' (although the manga was made in 1999)
* ''LightNovel/{{Baccano}}''
* ''Anime/BattleSpiritsShonenToppaBashin''
** ''Anime/BattleSpiritsShonenGekihaDan''
* ''Manga/{{Beelzebub}}''
* ''Manga/BlackLagoon''
* ''Manga/{{Bleach}}''
* ''Anime/BloodPlus''
* ''Anime/CasshernSins''
* ''Anime/CatSoup''
* ''Manga/{{Chobits}}''
* ''Manga/ChronoCrusade'' (Manga ran from 1998-2004)
* ''VisualNovel/{{Clannad}}''
* ''Manga/{{Claymore}}''
* ''Manga/CodeBreaker'' (manga, not the anime which came out in 2012)
* ''Anime/CodeGeass''
* ''Manga/DGrayMan''
* ''Manga/DNAngel (Manga began in 1997)''
* ''Manga/DansaiBunriNoCrimeEdge'' (the manga was released in 2009)
* ''Anime/DarkerThanBlack''
* ''Manga/TheDaughterOfTwentyFaces''
* ''Manga/DeathNote''
* ''Franchise/{{Digimon}}''
** ''Anime/DigimonAdventure02''
** ''Anime/DigimonFrontier''
** ''Anime/DigimonSavers''
** ''Anime/DigimonTamers''
* ''Anime/DuelMasters''
* ''Manga/ElementalGelade''
* ''Manga/ElfenLied''
* ''Anime/EurekaSeven''
* ''Manga/{{Eyeshield21}}''
* ''Manga/FairyTail''
* ''LightNovel/TheFamiliarOfZero''
* ''Manga/FarewellBelovedFalco''
* ''VisualNovel/FateStayNight''
* ''Manga/FullmetalAlchemist''
* ''Anime/FullmetalAlchemist'' (2003 anime adaptation)
* ''LightNovel/FullMetalPanic''
* ''Anime/GalaxyAngel''
* ''Anime/{{Gankutsuou}}''
* ''VideoGame/GateKeepers''
* ''Manga/GetBackers''
* ''Anime/GhostInTheShellStandAloneComplex''
** ''Ghost in the Shell Stand Alone Complex 2nd Gig''
* ''Manga/{{Gintama}}''
* ''Manga/GunslingerGirl''
* ''Manga/HajimeNoIppo'' (although the manga was made ten years prior)
* ''Manga/HekikaiNoAion''
* ''LightNovel/HaruhiSuzumiya'': Yamakan jumpstarting the Light Novel adaptation revolution.
* ''Manga/HayateTheCombatButler''
* ''Anime/HellGirl'' (the manga was made in 1997)
* ''Manga/{{Hellsing}}''
* ''Manga/HunterXHunter'' (although the anime began in 1999, the series gained its following in the 2000s)
* ''Manga/IkkiTousen''
* ''Manga/InuYasha'' (the manga began in 1996)
* ''Manga/IrisZero''
* ''Franchise/{{Jewelpet}}''
* ''Manga/{{KOn}}''
* ''Anime/KaleidoStar''
* ''Manga/KatekyoHitmanReborn''
* ''Literature/{{Kurozuka}}''
* ''Anime/LeChevalierDEon''
* ''Manga/LoveHina'' (although the manga was made in 1998)
* ''Manga/LoveLab'' (the manga, not the anime which came out in 2013)
* ''Manga/LovePistols''
* ''Manga/LuckyStar''
* ''Franchise/LyricalNanoha''
** ''Anime/MagicalGirlLyricalNanoha''
** ''Anime/MagicalGirlLyricalNanohaAs''
** ''Anime/MagicalGirlLyricalNanohaStrikerS''
* ''Manga/MahouSenseiNegima''
* ''Anime/MaiHime''
* ''Anime/{{Mai-Otome}}''
* ''LightNovel/MariaSamaGaMiteru''
* ''Anime/{{Mazinkaiser}}''
** ''Manga/MazingerAngels''
** ''Anime/ShinMazinger''
** ''ShinMazingerZero''
* ''Manga/MedakaBox''
* ''Anime/{{Metropolis}}''
* ''Manga/MidoriNoHibi''
* ''Manga/MinamiKe''
* ''Anime/MobileSuitGundam00''
* ''Anime/MobileSuitGundamSEED''
* ''Anime/MobileSuitGundamSEEDDestiny''
** ''[[Manga/MobileSuitGundamSEEDDestinyTheEdge GSD: The Edge]]''
* ''Anime/MobileSuitGundamUnicorn''
* ''Manga/{{Monster}}'' (the manga ran 1994-2001; the anime ran 2004-2005)
* ''Manga/{{Nana}}''
* ''Anime/{{NarueNoSekai}}''
* ''Manga/{{Narutaru}}'' (though the manga began in 1998)
* ''Manga/{{Naruto}}'' (although it actually began in 1999 and a one-shot was drawn in 1997, its first volume was released in 2000)
* ''Anime/OnegaiMyMelody''
* ''Anime/OnegaiTwins''
* ''Manga/OuranHighSchoolHostClub''
* ''Manga/PandoraHearts''
* ''Anime/ParanoiaAgent''
* ''Anime/PetitePrincessYucie''
* ''Anime/PleaseTeacher''
* ''Anime/PrettyCure''
** ''Anime/FutariWaPrettyCure[=/=]Max Heart''
** ''Anime/FutariWaPrettyCureSplashStar''
** ''Anime/YesPrettyCure5[=/=]Go Go''
** ''Anime/FreshPrettyCure''
* ''Manga/ThePrinceOfTennis'' (although the manga was made in 1999)
* ''Anime/PrincessTutu''
* ''Manga/{{Psyren}}''
* ''Anime/QueensBlade''
* ''Manga/RaveMaster''
* ''Anime/RentalMagica''
* ''Manga/RosarioToVampire''
* ''Manga/RozenMaiden''
* ''Manga/SaintSeiya''
* ''Manga/SaintSeiyaTheLostCanvas''
* ''Manga/SaintSeiyaNextDimension''
* ''Manga/{{Saiyuki}}''
* ''Manga/SakuraNoIchiban''
* ''Anime/SamuraiSeven''
* ''Manga/SayonaraZetsubouSensei''
* ''VisualNovel/SchoolDays''
* ''Manga/SchoolRumble''
* ''LightNovel/ScrappedPrincess''
* ''Anime/SeireiNoMoribito''
* ''Manga/{{Sekirei}}''
* ''LightNovel/ShakuganNoShana''
* ''Manga/ShamanKing''
* ''VisualNovel/{{Shuffle}}''
* ''Manga/SkipBeat''
* ''Manga/SoulEater''
* ''Anime/{{Stratos 4}}''
* ''Manga/SuperGals''
* ''Anime/SylvanianFamilies''
* ''Anime/TaiChiChasers''
* ''Anime/TengenToppaGurrenLagann''
* ''Manga/TenjhoTenge''
* ''Manga/ToLoveRu''
* ''LightNovel/{{Toradora}}''
* Franchise/{{Transformers}}
** ''Anime/TransformersRobotsInDisguise''
** UnicronTrilogy
*** ''Anime/TransformersArmada''
*** ''Anime/TransformersEnergon''
*** ''Anime/TransformersCybertron''
** ''Manga/KissPlayers''
* ''Manga/TsubasaReservoirChronicle''
* ''Manga/UltraManiac''
* ''Manga/VampireKnight''
* ''Anime/{{Vandread}}''
* ''Anime/{{Vipers Creed}}''
* ''Anime/VoicesOfADistantStar''
* ''Manga/TheWallflower''
* ''Manga/WanderingSon'' (manga, not the anime which came out in 2011)
* ''Manga/WarcraftTheSunwellTrilogy'' (2005-2007)
* ''Franchise/WhenTheyCry ''
** ''VisualNovel/HigurashiWhenTheyCry''
** ''VisualNovel/UminekoWhenTheyCry''
* ''Anime/{{Witchblade}}''
* ''Manga/WolfsRain''
* ''Manga/{{xxx Holic}}''
* ''Manga/YakitateJapan''
* ''Manga/ZatchBell''
* ''Anime/{{Zentrix}}''