We used a standardised behavioural surveillance survey (BSS), modified to be directly relevant to populations in conflict and post-conflict settings as well as to their surrounding host populations, to survey the populations of a refugee settlement in south-western Uganda and its surrounding area. Two-stage probability sampling was used to conduct 800 interviews in each population. The BSS questionnaire adapted for displaced populations was administered to adults aged 15–59 years. It collected information on HIV knowledge, attitudes and practices; issues before, during and after displacement; level of interaction and sexual exploitation among the refugees and host communities (i.e., nationals). Population parameters were compared and 95% confidence intervals were calculated for core HIV indicators. The demographic characteristics were similar (except for educational achievement), and HIV awareness was very high (>95%) in both populations. The refugees reported more-accepting attitudes towards persons with HIV than did nationals (19% versus 13%; p < 0.01). More refugees than nationals reported ever having had transactional sex (10% versus 6%; p < 0.01), which mostly occurred post-displacement. Five percent of females among both the refugees and nationals reported experiencing forced sex, which mostly occurred post-displacement and after the arrival of refugees, respectively. Nationals reported more frequent travel to refugee settlements than reported by refugees to national villages (22% versus 11%; p < 0.01). The high mobility and frequent interactions of these two populations suggest that integrated HIV programmes should be developed and would be an efficient use of resources. Evidence suggesting that female refugees may be at elevated risk for HIV infection, due to forced sex, transactional sex and other vulnerabilities, warrants further examination through qualitative research. The findings indicate a need for additional, focused HIV-prevention programmes, such as youth education, for both refugees and Ugandan nationals.