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The tallest of the penguins, Kowalski is second-in-command, forms plans for the group, and usually takes notes for Skipper. When Skipper is absent, he takes charge and his rank is First Lieutenant. He has blue eyes and tends to over-analyze situations.
Kowalski is part of a rookery of devious penguins who had made it their goal to escape captivity in the Central Park Zoo and leave for Antarctica. Often formulating plans for the group, Kowalski was a loyal supporter of his leader, Skipper. Kowalski had escaped the zoo with the other penguins but was promptly captured and put into a crate for transferring with his comrades. The crates were all placed on a ship bound for Africa, where all the creatures from the zoo would be kept in a wildlife preserve. While in the crate, Kowalski confessed that he could not read (he said the words on the side of the box were an "older code", in slight reference to Star Wars VI) and asked another transferee, a chimpanzee named Phil, to read the words on the crate. As soon as this was done, the four penguins headed to the ship's bridge, knocked out the crew and captain, bound them up, and Kowalski plotted the ship's course to Antarctica.
He is the technical one of the group and always has his notepad. While being able to formulate plans and invent things (such as a rocket ship out of a trashcan and fireworks, a rotary saw blade made of energy and multiple random objects, or a knowledge sucking the machine from just a cardboard box, a magnet, and a vacuum) he is shown to have a bit of difficulty deducing simpler machines. At the end of "Needle Point", it is revealed that he has an irrational fear of dentists, which is peculiar in that, as Private soon states after Kowalski runs off, penguins do not have teeth. He seems to also spout nearly or completely nonsensical words, such as, "The moo-cow may have a chocolate marshmallow", or "I'll be a bicycle cream cone", whenever either hit incredibly hard (as he did when body checked by a giant rat during a hockey game) or when shocked severely (as by Officer X's stun gun). He screamed "Galileo Galilei" when he got his injection during "Needle Point". He also loves candy.
In the series, he is shown to be intelligent but it is not as apparent in the films (e.g. in Madagascar he does not know how to read and in Madagascar: Escape 2 Africa he states that the paper plane would help them fly back to NY and he does not understand that the fuel indicator was indicating that fuel is finished). He does most of his calculations on an abacus, although he was briefly in possession of a calculator that was destroyed. He is in love with a dolphin called Doris and recorded a poem for her on DVD which highlighted her apparent non-interest in him in the "Hot Ice" episode. (She was first mentioned in "Gone in a Flash".)
Kowalski can play a banjo and sing as seen in Concrete Jungle Survival.
Kowalski reappears in Madagascar 3 and the 2014 movie Penguins of Madagascar as a major character.