Background A high prevalence of lifetime psychiatric disorders among help-seeking substance abusers has been clearly established. However, the long-term course of psychiatric disorders and mental distress among help-seeking substance abusers is still unclear. The aim of this research was to examine the course of mental distress using a six-year follow-up study of treatment-seeking substance-dependent patients, and to explore whether lifetime Axis I and II disorders measured at admission predict the level of mental distress at follow-up, when age, sex, and substance-use variables measured both at baseline and at follow-up are controlled for. Methods A consecutive sample of substance dependent in- and outpatients (n = 287) from two counties of Norway were assessed at baseline (T1) with the Composite International Diagnostic Interview (Axis I), Millon's Clinical Multiaxial Inventory (Axis II), and the Hopkins Symptom Checklist (HSCL-25 (mental distress)). At follow-up (T2), 48% (137/287 subjects, 29% women) were assessed with the HSCL-25, the Alcohol Use Disorders Identification Test, and the Drug Use Disorders Identification Test. Results The stability of mental distress is a main finding and the level of mental distress remained high after six years, but was significantly lower among abstainers at T2, especially among female abstainers. Both the number of and specific lifetime Axis I disorders (social anxiety disorder, generalized anxiety disorder, and somatization disorder), the number of and specific Axis II disorders (anxious and impulsive personality disorders), and the severity of substance-use disorder at the index admission were all independent predictors of a high level of mental distress at follow-up, even when we controlled for age, sex, and substance use at follow-up. Conclusion These results underscore the importance of diagnosing and treating both substance-use disorder and non-substance-use disorder Axis I and Axis II disorders in the same programme.