This study tests the general hypothesis that there is no single best way to organize a middle school to meet the variety of needs of early adolescent students. Using data from a sample of 433 schools in the Pennsylvania Educational Quality Assessment, it examines the effects of self-contained classroom instruction and departmentalization on two generally agreed-upon educational goals--positive student-teacher relations and high quality subject-matter instruction. The study finds self-contained classroom instruction benefits student-teacher relations at a cost to high quality subject-matter instruction, while departmentalization improves the quality of instruction in specialized subject matter at a cost to student-teacher relations. The same types of effects are proposed by analogy for scheduling and grouping practices. (Author)