Site differences in treatment outcomes are not often highlighted when the results of multisite randomized clinical trials (MRCTs) are reported. The primary analyses of a 6-site MRCT, the Treatment of SSRI-Resistant Depression in Adolescents (TORDIA) study, showed substantial variation by site in the performance of a medication-only condition and a combined medication plus cognitive-behavioral therapy (CBT) condition. Two potential primary causes of site differences in MRCT outcomes were examined in this article: sampling factors, particularly clinical characteristics of participants, and treatment protocol factors, particularly fidelity. The authors found that differences in the clinical characteristics of participants at baseline across site and within site/across conditions were the most salient explanations for site differences and differences within sites across conditions in outcome. Study findings are discussed with respect to the overall study outcomes in TORDIA as well as MRCTs in general. (Contains 2 tables, 2 figures and 1 footnote.)