Aims: To investigate the prognostic factors that determine 2-year outcomes in a group of alcohol-dependent patients with depression or bipolar disorder who were treated in an intensive 4-week inpatient programme. Methods: This was a longitudinal study of an inpatient treatment cohort of dual affective disorder and alcohol-dependent patients, in Dublin, Ireland. Measurements included baseline demographics with follow-up measurements at discharge, 3 months, 6 months and 2 years after treatment, including alcohol consumption, depression, mania/elation, anxiety, craving, drug use and sample blood tests. Factor and regression analysis of multiple variables was carried out to predict outcomes. Results: A total of 189 participants with alcohol dependence and comorbid depression (n = 101) or bipolar disorder (n = 88) were followed over 2 years after discharge from treatment. Retention rate was 76% over 2 years. Early abstinence (at 6 months) predicted better abstinence overall at 2 years; and bipolar alcoholics had a better outcome in drinks per drinking day than depressed alcoholics at 2 years. Younger participants (age 18–30 years) did relatively worse than middle-age (30–50 years) and older (51 + years) participants in measures of abstinence and number of drinks per drinking day at 2 years; and females did better than males in number of drinks per drinking day at 2 years. Conclusion: Dual diagnosis of alcohol dependence and depression or bipolar disorder may be treated together with intensive intervention and follow-up, and various prognostic factors including early abstinence emerge over time that influence outcomes over 2 years.