Medical school is an academic and developmental path toward a professional life demanding self-regulation and self-education. Thus, many medical schools include in their goals for medical student education their graduates' ability to self-assess and self-regulate their education upon graduation and throughout their professional lives. This study explores links between medical students' use of self-regulated learning as it relates to motivation, autonomy, and control, and how these influenced their experiences in medical school. Subjects were medical students in two distinct medical school environments, "Problem-based learning" and "Traditional." PBL students described a rough transition into medical school, but once they felt comfortable with the autonomy and control PBL gave them, they embraced the independence and responsibility. They found themselves motivated to learning for learning's sake, and able to channel their motivation into effective transitions from the classrooms into the clerkships. Traditional students had a rougher transition from the classrooms to the clerkships. In the first two years they relied on faculty to direct and control learning, and they channeled their motivation toward achieving the highest grade. In the clerkships, they found faculty expected them to be more independent and self-directed than they felt prepared to be, and they struggled to assume responsibility for their learning. Self-regulated learning can help smooth out the transitions through medical school by preparing first and second year students for expectations in the third and fourth years, which can then maximize learning in the clinical milieu, and prepare medical students for a lifetime of learning.