This paper investigates gender differences in the associations between adolescent mode choices and travel patterns for the trip to school and levels of physical activity. Analysis relies on cross-sectional data collected from adolescents (N = 269) in Baltimore City for a school-based recruitment study of physical activity and the built environment. Participants were recruited from two magnet high schools, comprising a predominantly African-American sample (67%) with geographically disperse home locations. Data analyzed here for each individual include (a) a web-based survey that collects background information, attitudes, perceptions, and recall behavior, (b) week-long physical activity data collected by accelerometers, (c) a week-long travel diary, (d) archived spatial data about the built environment around each student's primary home address, and (e) height and weight measurements, used to calculate body mass index (BMI). Multinornial logit models of the primary mode to school were estimated separately for males and females. Results show key differences in the factors associated with their travel choices. Aggregate levels of physical activity during the weekday for transit commuters and auto commuters were compared for males and females. Results show significantly higher levels of physical activity for both male and female students who commute by transit, although male physical activity levels were higher on average. There were no significant differences in BMI between transit and auto commuters by gender, however.