DENVER — A federal judge on Tuesday asked the US State Department to reconsider its decision to deny a passport to a Colorado resident who does not identify as either male or female and refused to check a box for one of the genders on the passport application form.

US District Judge R. Brooke Jackson ruled the State Department did not show that it acted rationally in refusing to give a passport to Dana Zzyym, who was born with ambiguous sexual characteristics and sued the State Department after being denied a passport.

However, the judge said he wanted to give the State Department an opportunity to reconsider its decision or present justification to back it up.

Jackson said the court would not weigh in on the constitutionality of the issue ‘‘unless and until it needs to.’’

Zzyym’s parents, in consultation with doctors, decided to raise their child as a boy. Zzyym praised the judge’s ruling but called it the ‘‘first step in a long battle.’’

Associated Press