Background/Context: There is general agreement that most public high schools should be smaller than they are. Although the small-schools movement attracts considerable support, there is a general reluctance or inability to close large schools and to build many new small schools. A more cost-effective approach is to divide larger high schools into several smaller units, typically called schools within schools (SWS). We use the term subunit to describe these smaller educational groupings, which are generally organized around themes, careers, or pedagogical approaches intended to appeal to students' interests and future plans. The majority of SWS designs then allow students to select their subunits. As such, the SWS model represents a convergence of two popular reform efforts--the movement to create smaller high schools, and the push to increase educational choice. Purpose/Objective/Research Question/Focus of Study: This article addresses three questions related to academic differentiation and student choice within SWS high schools. First, to what extent did subunit themes emphasize students' disparate occupational and educational futures over their common social and academic needs? Second, what rationales did students offer for their subunit selections, and how did their choices reflect their interests, motivations, social backgrounds, and academic abilities? Third, how can we characterize the interplay between subunit offerings, students' subunit choices, and educational equity? Research Design: This article draws on data collected over several years in a sustained field-based study of five SWS high schools. Our data collection included conducting individual and focus group interviews with students, teachers, guidance counselors, and school- and district-level administrators; shadowing students; visiting selected classrooms; observing interactions in hallways and other public locations; attending special events that occurred during our visit; mapping the physical layout of the building; collecting papers and documents pertinent to school life; and learning about the contexts in which the school operated. Conclusions/Recommendations: Each school offered subunits organized around academic subjects, career focuses, or pedagogical approaches. Certain subunits were designed for students seeking traditional vocational training, whereas others targeted academically motivated college-bound students. Although students ostensibly selected subunits that matched their interests and motivations, varied social and structural pressures beyond subunit themes influenced their choices. As a result, to varying degrees within schools, subunits were segregated and stratified by student race/ethnicity, social class, and--above all--academic performance. With stark parallels to student curricular choice in comprehensive high schools, many school staff viewed these within-school divisions as the natural (and even appropriate) outcome of student social and academic difference.