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Background  Little research addresses how medical students develop their choice of specialty training in crisis and resource-poor settings. The newly graduated medical students determine the future of the healthcare system. This study aims to elucidate the factors influencing Syrian medical students’ specialty selection and students’ intentions to study abroad.    Methods  A cross-sectional study carried out at the universities of Damascus, Al-Kalamoon and the Syrian Private University in Syria using self-administered questionnaire to investigate medical students’ specialty preferences and plans for career future. The questionnaire included questions about students’ demographic and educational characteristics, intention to train abroad, the chosen country for training.    Results  Randomly selected 450 students completed the questionnaire. The two most common specialties selected were general surgery (27.6%) and internal medicine (23.5%). The most influencing factors on their decision were ‘flexibility of specialty’ (74.8%) and ‘Better work opportunities after specializing’ (69.1%). Most participants stated that they are interested in specializing abroad outside Syria (78.7%). The two most common countries of choice were Germany (35.5%) and the United States of America (24.6%). Acquiring a visa to the foreign country was the most common obstacle of specializing abroad ( n  = 186, 53.6%). Male gender, having a previous clinical training abroad, and having friends or relatives living abroad were significant factors in predicting students’ interest in specializing abroad.    Conclusion  Internal medicine and surgery are the most reported specialties of choice in this study and most of the participants reported intentions to study abroad. Their specialty preferences are influenced by both familiar epidemiological and war-driven factors. These data can be useful to design further cohort study to understand the war-related affecting factors on students’ plans for their career in the effort of improving the balance of healthcare system in Syria.    Electronic supplementary material  The online version of this article (10.1186/s12909-018-1146-x) contains supplementary material, which is available to authorized users.

Specialty preference and intentions to study abroad of Syrian medical students during the crisis