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Aside from giant Pokémon, many Pokémon in the Pokémon anime suffer from large size discrepancies between the information given in the Pokémon games' Pokédex and their actual animated presentation. These Pokémon are apparently "normal sized" as far as the anime's universe is concerned. Many of Ash Ketchum's Pokémon are often subject to size discrepancies, often appearing smaller than other Pokémon of the same species.
This may be a style or aesthetic decision, a case of the writers not checking the information in detail, or for story purposes.
Some of the most notable size discrepancies will be noted below.
Articuno are about 5'07" (1.70m), although in The Symbol Life it appears to be closer to 6'07" (2m).
Blastoise are normally 5'03" (1.60m) tall, while in the anime they appear closer to 6'03" (1.90m) tall.
Bulbasaur are about 2'04" (70cm), similar in height to Buizel. In anime episodes, it appears closer to 1'04" (40cm).
Charizard are usually 5'7" (1.7m) tall, but Ash's Charizard is taller than that, at about 7'00" (2.10m) tall. Oddly enough, it is shown in Charizard's Burning Ambition that Ash's Charizard is rather small when compared with the Charizard living in Charicific Valley. Also, in Grating Spaces!, a Charizard was shown to be as tall as an Aggron, 6'11" (2.10 m).
Croagunk are generally 2'04" (70cm) in height, with an anime height closer to 1'04" (40cm).
Drapion are generally 4'03" (1.30m) in height, but in the anime, they are about twice that height.
Dunsparce are normally 4'11" (1.5m) in height, approximately the height of Ash. In Following a Maiden's Voyage!, they appear to be shorter than a Pidgey, which is 1'00" (30cm). However, this may also be due to the measurement being from head to tail instead, making the mistake slightly less drastic.
Electivire are normally 5'11" (1.80m), but in the anime they are closer to 6'11" (2.10m).
Electrode are normally 3'11" (1.20m), but in What You Seed is What You Get! it is seen to be the same height as Slugma, 2'04" (70cm).
Also, in What You Seed is What You Get, Natasha's Electrode is shown to be as tall as an adult human in some scenes.
Emboar is normally 5'03" (1.60m) tall. However, Bianca's Emboar is shown to stand several heads above her, making it appear closer to 7'02" (2.18m).
Floatzel are generally 3'07" (1.10m) in height, but in A Crasher Course in Power!, when Crasher Wake's was standing in front of Ash's Buizel, it was shown to be about 4'03" (1.30m).
Forretress measures 3'11" (1.20m) tall, but it is sometimes shown in the anime to be 1'08" (50cm).
Gabite are normally 4'07" (1.40m) in height, but Ursula's Gabite from Another One Gabites the Dust! was at least a couple inches taller than Ash, Dawn, and Ursula, who can be thought to be around 5'0" (1.50m) tall.
Gengar are shown to be 4'11" (1.50m), but in all of its appearances in the anime, it is shown to be 3'07" (1.10m).
Glalie are 4'11" (1.50m). Ash's Glalie is extremely small compared to others of its species, appearing to be closer to 2'00" (60cm).
Golduck are about 5'07" (1.70m), although in Like It or Lup It! when it was standing near Ludicolo, it was shown to be about 3'03" (1m).
Grovyle and Combusken
While normally Grovyle and Combusken are about 2'11" (90cm), Ash's Grovyle and May's Combusken appear to be much larger, being almost as tall as Ash and May. Assuming that Ash is about 5'0" (1.50m), that estimates Grovyle and Combusken to be around 4'0" (1.20m). The other Grovyle that have appeared were around this size as well.
Hariyama are 7'07" (2.30m). However, Brawly's Hariyama is extremely small for its species. In Brave The Wave!, it appears to only be around 4'11" (1.50m).
Lombre are shown to be 3'11" (1.20m). Brock's Lombre appears to be shorter than that height, and looking to be more around 2'07 (80cm).
Magmortar are normally 5'03" (1.60m), but in the anime they are closer to 7'00" (2.10m).
Metagross are normally 5'03" (1.60m), but Tyson's seems shorter than this in Choose It or Lose It!, at 2'11" (90cm). Another Metagross appeared in Noodles! Roamin' Off! and shown to be taller even than James, about 6'03" (1.90m).
Noctowl are about 5'3" (1.60m), approaching average human height. Ash's Noctowl, however, is extremely small for that size, looking to be more around 2'00 (60cm). Although it's been mentioned that Ash's Noctowl is unusually small, the other two Noctowl that have appeared in the anime don't seem to be more than 4'0" (1.20m) tall.
Nosepass are normally 3'3" (1m) in height. However, in the episode Nosepass debuted in, Nosepass is far bigger than it is supposed to be, at about 5'6" (1.70m) compared to the normal Nosepass.
Onix is already one of the largest Pokémon at 28'10" (8.8m) long, but in Climbing the Walls!, Grant's Onix was sometimes shown to be twice that size.
Pidgeotto are normally 3'07" (1.10m), but in the series it appears to be only 2'04" (70cm).
Rapidash are normally 5'07" (1.70m). However, in Ash's flashback in Strategy Begins at Home!, it was shown to be about 3'03" (1m) tall, about the size of a Ponyta.
One of the more renowned changes in size is in Roselia, which are extremely small—only about a foot (30cm) tall. However, the Roselia in the anime come up to a 10-year old's waist. An estimate would put the anime incarnation of them at about 3' (90cm) tall. This caused much confusion when Pokémon Colosseum and Pokémon Adventures both featured the Pokémon at its actual smaller size.
Jessie's Seviper appears to change sizes during the series, sometimes even in the same episode. For example, when it made its debut, it was shorter than Jessie. However, it has also been shown as being taller than her, which according to the Pokédex it should be.
Smeargle are about 3'11" (1.20m), although in Art of Pokémon it is shown to be 2'04" (70cm).
Togekiss are 4'11". Dawn's Togekiss, in its episode debut, was shown to be slightly taller than Dawn. In all episodes since, it has been shown to approach close to her hip.
Wailmer are generally 6'07" (2m) in height, although the one in Leading a Stray! was shown to be more than twice the size of Ash, who is approximately 5'0" (1.50m) tall, therefore making it more than 10'0" (3m) tall.
Whismur are small Pokémon at around 2'00" (60cm). In A Pokéblock Party!, a Whismur was around the size of 1'00" (30cm), and was noticeably not much larger than Max's head. A second Whismur appeared in Pinch Healing! and, while standing, came up to Max's neck.