Pedagogical practices such as active learning and group-based exercises are increasingly being used to engage students in course content during class meetings. However, techniques employed in class may not always contribute to engagement outside of the class meetings, or to student satisfaction with the course itself. Previous reports have shown that student autonomy and initial perceptions of the course setup influence their engagement and satisfaction, independent of the course context. To address engagement in an upper level collegiate biology class, students were allowed to choose their own assignments accounting for 50% of their total grade and also choose the due dates for those assignments; the remaining 50% came from exam scores. The goal was to allow students the option to pick assignments that best reflected their perceived strengths and preferences in order to determine whether these options increased students' satisfaction and engagement with the course content. Students were surveyed with questionnaires at the beginning and end of the semester to monitor their perception of the course setup, their interest in the course content, and their satisfaction with the course. Comparing initial perception of the course layout with final experiences, students reported that assignment choice did increase interest in the course and resulted in a student-reported increase in personal responsibility within the course.