There is a persistent shortage of qualified health workers globally, but worse in developing countries, where it is even worse in rural areas than urban and peri-urban areas. Health workers refuse to be deployed in rural areas or migrate to urban areas in search of better physical facilities and to avoid professional isolation, among other reasons. Health workers brought up in urban areas have not experienced rural life and find it difficult to countenance a professional life in rural areas. Several training institutions have engaged in programmes to expose pre-service health workers to rural health work to demystify it and to enable the professionals make an informed choice on practice location after qualification. In this study, the intentions of Ugandan medical students to work in rural health facilities after qualification were sounded out, together with the factors that affect them and their perception of rural areas. The study covered five government medical schools (2 for doctors and 3 for Clinical Officers). Students of all years of study in the different courses were interviewed, as well as key informants in the administration of the schools. At least one half of all the respondents (50% or 167/336) were clear that they did not intend to work in the rural facilities after training, while the other half was divided equally among those who wanted and those who were not sure yet. Whereas the proportion of those intending to work in rural areas rose progressively from the first year of studies, it reached a peak in the pre-final year (fourth year for student doctors and second year for clinical officers) and plummeted in the final year after the students had residential field experience. The majority of the students had a negative perception about working in the rural areas and associated them with lack of physical facilities, social services and communication. Personal demographic characteristics and previous exposure to a rural life did not seem to be related to a choice about work in rural areas. Most of the few students who intended to work in rural areas hoped to stay for not more than three years, before going either for further studies or for self-employment in urban areas.