Many hypotheses have been put forth regarding the reasons for the under-representation and under-performance of women in physics. While prior work has focused on the relations between students' prior knowledge and performance outcomes, less work has examined student motivation. To gain a better understanding of male and female students' motivational characteristics during instruction, we conducted a longitudinal study that evaluated students' self-efficacy, grit, fascination and value associated with physics, intelligence mindset, and physics epistemology at three points during two-semester introductory physics sequences. Females reported lower self-efficacy than males at the beginning of the year and those self-reports remained lower throughout the sequence. In addition, females' fascination and value associated with physics decreased more than those of males throughout the sequence. By the end of the sequence, females were also more likely than males to endorse the view that physics intelligence is a "fixed" ability. Implications for the design and implementation of effective instructional strategies are discussed.