Middle school students classified with Emotional Disturbance in two levels of least restrictive environments (LRE)--self-contained classes (SCC) and a self-contained school (SCS)--were compared at the beginning and the end of a school year, using demographics, IQ and achievement testing, a teacher checklist for DSM-IV psychopathology, and standard measures of school functioning. At baseline the SCS students were significantly lower in both IQ and achievement than the SCC group and were significantly higher in the occurrence of externalizing psychopathology. Overall, reading achievement and oppositional-defiant symptoms were the baseline variables that best separated these two groups. Longitudinally, SCC students functioned significantly better than the SCS students over one school year. However, while the SCC levels of psychopathology generally worsened, the SCS group improved overall, with significant changes in the oppositional defiant and generalized anxiety symptom categories. Consequently, students in these two LREs were different both academically and behaviorally, at both baseline and longitudinally, with implications to improve their education and treatment. (Contains 4 tables.)