Apparently,
Back when type was made out of individual metal letters, it was organized in two separate wooden cases. You guessed it! At the printer, where a page was set one letter at a time, capital letters were stored in the “upper case,” and the small letters were kept in the one underneath, called the “lower case.”
Another little-known fact: The uppercase forms are derived from letterforms chiseled into the top part of a Roman monument, building, or pillar called a “capital.” Hence the term capital letters.
from my typography class at sessions.edu