To investigate differences in learning gains by gender, we collected data in large introductory astronomy and biology courses. Male astronomy students had significantly higher pre- and post-test scores than female students on the astronomy diagnostic test. Male students also had significantly higher pretest and somewhat higher post-test scores than female students on a survey instrument designed for an introductory biology course. For both courses, males had higher learning gains than female students only when the normalized gain measure was utilized. No differences were found with any other measures, including other gain calculations, overall course grades, or individual exams. Implications for using different learning gain measures in science classrooms, as well as for research on learning differences by gender are discussed.