Clowes was born in Chicago, Illinois, to an auto mechanic mother and a furniture craftsman father. His mother was Jewish, whereas his father was from a "reserved WASPish Pennsylvania" family; Clowes's upbringing was not religious. In 1979, he finished high school at the University of Chicago Laboratory Schools and attended the Pratt Institute in Brooklyn, New York, where he earned a BFA in 1984. It was at Pratt that he met and befriended fellow cartoonist Rick Altergott, with whom he started the small-press comics publisher Look Mom Comics.
According to Clowes scholar, Ken Parille, the cartoonist had an early response to a "graphic" comic when, at age four, he burst into tears and began hitting his head against a wall after seeing a cover of a Strange Adventures comic book that depicted a family dying of heat. Later, he received "piles of 1950s and 1960s classic titles like Archie and The Fantastic Four" from his older brother, who also introduced him to the work of legendary cartoonist R. Crumb. [Wikipedia]