Co-occurrence of alcohol dependence with other mental disorders is very common, being important cause of diagnostic and therapeutic difficulties. There is a lack of systemic solutions in mental health care dedicated to the patients with dual diagnosis. The literature on the topic of treatment of patients with dual diagnosis is limited. While comorbidity of alcohol dependence with mental disorders is prevalent, there is rising interest among researchers on that issue. In this paper we present current hypotheses on pathogenesis of dual diagnosis as well as recommendations for its treatment. The role of disturbances in functioning of hypothalamic-pituitary-adrenal axis in pathogenesis of co-occurrence of alcohol dependence with anxiety and affective disorders is presented. Researchers studying dual diagnosis underline the fact that simultaneous treatment of alcohol dependence and co-occurring psychiatric disorders increases the chance to improve patients` functioning. Inappropriate treatment without complete management of all existing problems may make full recovery impossible.