This paper reviews the results of an acute phase trial and a five-year follow-up study of fluoxetine in adolescents with major depression and a substance use disorder (SUD). This study included a 12-week open label acute phase study of 13 comorbid adolescents, followed by comprehensive assessments conducted 1, 3, and 5 years after entry into an acute phase fluoxetine trial. The results of the acute phase study and of the 1, 3, and 5-year follow-up assessments have already been published in four papers. The current paper was designed to cover the results of the study across the entire 5-year time spectrum of the study, and to summarize the clinical results across that entire time period. The data from this pilot study suggest that the long-term (5-year) clinical course for the Alcohol Dependence, Cannabis Dependence, and academic functioning of comorbid adolescents following acute phase treatment with SSRIs is generally good. However, the long-term clinical course for the Major Depression of that comorbid adolescent population is surprisingly poor.