Purpose With over 20 million refugee women in the world today, health of refugee women has significant global health implications. Women affected by humanitarian crisis have significant trauma related mental health concerns that may affect reproductive health. The purpose of this study was to test the hypothesis that poor mental health status impinges upon reproductive health service use within the population of refugee women living in temporary camps and settlements. Methods This study consisted of 1) psychometric validation of the Self Report Questionnaire (SRQ) and the Self Report Questionnaire-Suicide Ideation and Behavior (SRQ-SIB), 2) a mixed methods analysis of cross-sectional data and 3) data reduction of the SRQ-SIB, using data from the Reproductive Health Assessment for Conflict Affected Women survey conducted among Congolese refugee women in the summer of 2008. A qualitative component was added post hoc with interviews and written communication with key informants. The sample size was 810 participants. Results The SRQ and the SRQ-SIB demonstrated a high level of reliability at .911 for both scales. Predictive validity revealed a highly significant model for both instruments in relation to women who experienced sexual violence. While the mean score on the SRQ-SIB was 6.2 (SD=5.6), women who had experienced a traumatic event or reported suicidal behavior had much higher mean scores; 8.2(SD=5.8) and 14.1(SD=5.5) respectively. Antenatal care rates were high (90%), as were HIV screening rates (81%); alternatively, family planning use (11%) and sexually transmitted infection (STI) treatment seeking (7%) were low among those at risk. No significant associations were found between mental health status and reproductive health service use. Qualitative interviews revealed that while reproductive health service use was strongly encouraged, mental health assessment and care were not available. Conclusion This study provides details on mental health status and reproductive health service use in Rwandan refugee camps. Reproductive health is broadly available and reaches most women for HIV testing and antenatal care. Prevalence of common mental disorders (CMDs) in this sample was high. The SRQ-5 may be a useful and important tool in the clinical setting for quickly assessing women in crisis situations for CMDs and suicidal behavior.