Background/Aims: Differences in the clinical presentation of men and women with borderline personality disorder (BPD) are of potential interest for investigations into the neurobiology, genetics, natural history, and treatment response of BPD. The purpose of this study was to investigate gender differences in axis I and axis II comorbidity and in diagnostic criteria in BPD patients. Methods: 110 women and 49 men with BPD were assessed with the computer-based version of the Munich-Composite International Diagnostic Interview and the Structured Clinical Interview for DSM-IV Personality Disorders. Gender differences were investigated for the following outcomes: (a) lifetime, 12-month and 4-week prevalence of axis I disorders; (b) axis II disorders, and (c) DSM-IV BPD diagnostic criteria. Results: With regard to lifetime prevalence of axis I disorders, men more often displayed a substance use disorder, in particular alcohol dependency (65 vs. 43%); on the other hand, women more frequently had an affective (94 vs. 82%), anxiety (92 vs. 80%) or eating disorder (35 vs. 18%), in particular anorexia nervosa (21 vs. 4%). Regarding the 12-month prevalence, we found significantly more women suffering from anorexia nervosa (13 vs. 0%). Considering the 4-week prevalence, there were no significant gender differences. With regard to axis II disorders, men had a higher frequency of antisocial personality disorder (57 vs. 26%). Regarding the BPD diagnostic criteria, men more often displayed ‘intensive anger’ (74 vs. 49%), whereas women more frequently showed ‘affective instability’ (94 vs. 82%). Conclusion: In this German study, we could replicate and extend the findings from previous US studies, where men and women with BPD showed important differences in their pattern of psychiatric comorbidity. The implications for clinicians and researchers are discussed.