Objective: Securing a sufficient number of medical residents to work in rural areas is an urgent issue. This study sought to clarify the factors that cause medical students at a rural university in Japan to select a particular place for their initial clinical training.Materials and Methods: A questionnaire was administered to all medical students at Saga University between February and March 2021. Participants were divided into two groups based on their training location choice: those who chose Saga Prefecture (Saga group) and those who selected other prefectures (non-Saga group). Then, logistic regression analysis was performed.Results: The questionnaire was answered by 300 students (46.3% response rate), of whom 291 agreed to participate in the study; 122 (41.9%) and 169 (58.1%) students were allocated to the Saga and non-Saga groups. Within the Saga group, the following factors were statistically significant: being admitted to Saga University’s medical school through the system of special allotment of admission to applicants pledging to work in Saga Prefecture following graduation (or regional quota programs for admission) (odds ratio [OR], 19.18; 95% confidence interval [CI], 6.99–52.60); and being from Saga Prefecture (OR, 6.05; 95% CI, 2.24–16.35). With the non-Saga group, the desire to work in an urban area (OR, 0.03; 95% CI, 0.00–0.37) was statistically significant.Conclusion: To encourage medical residents to choose this prefecture for their initial clinical training, the focus should be on medical students who are from Saga Prefecture or admitted through the regional quota program.