Background Depressed and bipolar alcoholics represent a significant affective subgroup that has a poorer prognosis than either diagnosis alone. To date few systematic treatment programs have been developed to treat dual diagnosis. Methods An inpatient treatment program was developed at St Patrick's Hospital Dublin to treat dual diagnosis clients with alcohol dependence and either unipolar or bipolar affective disorder. Clients ( N = 232) were assessed for depression, anxiety, elation, cravings, drink and drug intake on admission, discharge, 3 and 6 months post-discharge from the program. Results In the overall group there was a reduction in number of drinking days and units per drinking day over the study ( p < .01). There was a 71.8% complete abstinent rate at 3 months and 55.8% at 6 months in the depression group, non-significantly greater than for the bipolar group at 64.7% and 54.1% respectively. Gamma GT, MCV and craving scores were significantly reduced over time ( p < .01). Mania, depression and anxiety inventory scores fell over time in both groups ( p < .01). 15–21-year olds were more severely anxious, had higher illicit drug use, and were more likely to relapse to drug use than older clients. Bipolar 1 clients were significantly more likely than bipolar 2 clients to be on mood stabilisers at all follow-up stages ( p < .001). Limitations No control group was used. Conclusions There is evidence for efficacy of a specifically designed dual diagnosis inpatient treatment program as both depressed and bipolar alcoholics had significant reductions in all measurements of mood, craving, and alcohol/drug consumption by self report and biological markers, suggesting both diagnoses can be effectively treated together.