Aim To assess the prevalence and gender characteristics of psychological health problems of raped individuals during the Bosnia-Herzegovina (BH) 1992–1995 war sixteen years after war quitted. Method The study was carried out in BH, in January 2011. We assessed 95 (81 females) Bosniac (Muslim) war survivors who experienced raping as a tool of genocide, aged 50 ± 10.1 years (min. 32, max. 73 years), without gender significant differences for presence of posttraumatic stress disorder (PTSD), anxiety disorder, depression, somatic symptoms, anxiety and insomnia, social dysfunction, severe depression, prevalence of smoking and alcohol drinking. We used Harvard Trauma Questionnaire (HTQ), Hopkins Symptom Checklist (HSCL-25) and General Health Questionnaire (GHQ-28). Results Respecting the DSM-IV criteria, in the whole sample of 95 raped victims, 90 (94.7%) met criteria for PTSD, 94 (98.9%) for anxious disorder, 93 (97.9%) for depression, 73 (76.8%) for somatic symptoms, 75 (78.9%) for anxiety and insomnia, 55 (57.9%) for social dysfunction, 53 (55.8%) for severe depression, 53 (55.8%) were cigarette smokers and 8 (8.4%) drunk alcohol. Women significantly more frequent presented anxious disorder 81 (100%) than amongst men 13 (92.9%), while men significantly more drunk alcohol than women (Chi-Square=5.847, P = 0.016; Chi-Square=15.635, P Conclusions Raped women were significantly more often anxious than men and raped men significantly more often drunk alcohol than women. There were no significant gender differences in the prevalence of PTSD, depression, somatic symptoms, anxiety and insomnia, social dysfunction, severe depression and smoking cigarettes amongst raped war survivors.