OBJECTIVE: An ongoing study of phenotypes of alcohol dependence among Alaska Natives provides the opportunity to investigate gender differences in reported health-related problems among alcohol dependent clients in three residential programs in Anchorage, Alaska. METHOD: Clinical assessment information was obtained on 469 (263 male) subjects from consecutive admissions to each of three treatment programs. The average (SD) age of the sample was 33.7 (8.4) years. Patterns of substance use, comorbid psychopathology, overall health status, alcohol and other drug withdrawal symptoms, and psychological and physical consequences of alcohol and other drug use were examined. RESULTS: Male and female subjects reported similar experiences with alcohol-related health problems, including symptoms of withdrawal and the psychological and physical consequences of chronic alcohol abuse. However, women were significantly more likely to have lifetime diagnoses of major depression and cocaine dependence, whereas men were more likely to have lifetime diagnoses of antisocial personality disorder and marijuana dependence. Women reported a lower overall health status, more medication use and pain complaints, and more negative consequences of cocaine abuse and withdrawal than did men. CONCLUSIONS: Both men and women within this sample of inpatient alcohol-dependent Alaska Natives were found to have a similar early onset and rapid progression to DSM-III-R alcohol dependence, and to report a similar prevalence of alcohol-related psychological and physical problems. Reports by women of more pain symptoms, more medication use and more negative health consequences related to their cocaine abuse, compared with men in this alcohol dependent sample, suggests additional considerations for treatment planning and intervention.