BACKGROUND: Providing reproductive and sexual health services is an important and challenging aspect of caring for displaced populations, and preventive and curative sexual health services may play a role in reducing HIV transmission in complex emergencies. From 1995, the non-governmental "Reproductive Health Group" (RHG) worked amongst refugees displaced by conflicts in Sierra Leone and Liberia (1989-2004). RHG recruited refugee nurses and midwives to provide reproductive and sexual health services for refugees in the Forest Region of Guinea, and trained refugee women as lay health workers. A cross-sectional survey was conducted in 1999 to assess sexual health needs, knowledge and practices among refugees, and the potential impact of RHG's work. METHODS: Trained interviewers administered a questionnaire on self-reported STI symptoms, and sexual health knowledge, attitudes and practices to 445 men and 444 women selected through multistage stratified cluster sampling. Chi-squared tests were used where appropriate. Multivariable logistic regression with robust standard errors (to adjust for the cluster sampling design) was used to assess if factors such as source of information about sexually transmitted infections (STIs) was associated with better knowledge. RESULTS: 30% of women and 24% of men reported at least one episode of genital discharge and/or genital ulceration within the past 12 months. Only 25% correctly named all key symptoms of STIs in both sexes. Inappropriate beliefs (e.g. that swallowing tablets before sex, avoiding public toilets, and/or washing their genitals after sex protected against STIs) were prevalent. Respondents citing RHG facilitators as their information source were more likely to respond correctly about STIs; RHG facilitators were more frequently cited than non-healthcare information sources in men who correctly named the key STI symptoms (odds ratio (OR) = 5.2, 95% confidence interval (CI) 1.9-13.9), and in men and women who correctly identified effective STI protection methods (OR = 2.9, 95% CI 1.5-5.8 and OR = 4.6, 95% CI 1.6-13.2 respectively). CONCLUSION: Our study revealed a high prevalence of STI symptoms, and gaps in sexual health knowledge in this displaced population. Learning about STIs from RHG health facilitators was associated with better knowledge. RHG's model could be considered in other complex emergency settings.