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(customize-set-variable case-fold-search  nil)

Or bind that variable (option) in your own command that is otherwise just a wrapper around query-replace. This has the advantage that it doesn't change the variable value for general use, outside of query-replacing.

See also variable case-replace, which controls case for the replacement text.

See also C-h f query-replace, where it says, for example:

Matching is independent of case if case-fold-search is non-nil and FROM-STRING has no uppercase letters. Replacement transfers the case pattern of the old text to the new text, if case-replace and case-fold-search are non-nil and FROM-STRING has no uppercase

See also the comments below, and Emacs bug #20687, where show how you can patch perform-replace to let you toggle case folding during query-replace.

Note too that the existing code for perform-replace binds case-fold-search in this way (note the variables on which it depends):

(case-fold-search  (if (and case-fold-search search-upper-case)
                       (isearch-no-upper-case-p from-string regexp-flag)
                     case-fold-search))