The School District of Philadelphia's tiered system of selective, nonselective, and charter high schools, and the process for high school choice, has created real variation in the degree to which high schools can successfully meet the needs of ninth graders. Research has shown that the ninth grade year is critical in determining a student's likelihood of graduating from high school. This mixed-methods study examines the transition to high school in Philadelphia, which we define as including the eighth grade high school selection process and students' experience in their ninth grade year. In our analysis of eighth grade applications to district-managed high schools for the 2007-08 school year, we found that most District eighth graders participated in the high school selection process, but fewer than half of them were admitted and enrolled in any of their chosen schools. Further, comparing across types of high schools, we found first, that the choice process contributes to system stratification, with low-income students, Black and Latino students, students who need special supports, and boys concentrated in nonselective neighborhood high schools and Whites, Asians, and girls concentrated in special admission high schools. Second, we learned that the choice process creates distinct challenges to the neighborhood schools' ability to support ninth graders. Enrollment at neighborhood high schools does not settle until the school selection process settles in late summer, and then continues to shift through the fall due to geographic mobility and returns from the juvenile justice system or other schools. Late enrollments undercut the ability of the neighborhood high schools to prepare for incoming classes, and contribute to changes in course schedules and teacher assignments after the school year begins, which cost important instructional time. Finally, we found that despite widespread acknowledgement of the importance of the freshman year, competing district agendas often mean it is not a priority in district and school planning. Freshman year interventions are often implemented piecemeal, without the professional support teachers need to adopt new practices, and without the assessments needed to know if they are effective. We argue that if low-performing neighborhood high schools are going to "turn around" or improve, it will require not only building school capacity but also implementing changes to the broader systems of district policy and practice in which these schools function, including the high school selection process.