Introduction : The Syrian crisis started 9 years ago causing substantial damage to the country’s infrastructure, and the consequences of this tragedy have further stunted the underdeveloped research environment in Syria. This paper aims to address the challenges of conducting medical research among Syrian academics during the Syrian crisis. Methods: The data were collected from (471) Syrian researchers (MsC or PhD students, university professors) from 13 universities and hospitals, covering 10 governates. A questionnaire was developed to collect the data and 52 factors were identified as research challenges. Results: The main institutional challenges are: (94%) insufficient funding, (80.3%) difficulties in acquiring supplies and equipment, (79.6%) lack of neutrality in approving research proposals. In regards to the personal challenges, (70.1%) expressed a high level of motivation to carry out research but only (33.4%) are confident that they have enough knowledge, (53.1%) do not have academic writing skills, (73.5%) do not have the basic information about medical statistics. For the crisis related factors, (83.5%) cite collecting data and reaching the sources of data as the main challenge, (80.4%) for losing contact with the patients because of the war situation, (76.3%) for lack of governmental support for the research during the crisis. Conclusion: Syrian medical researchers continue to face a number of challenges and the Syrian crisis has brought more problems and obstacles to the surface. However, despite those numerous challenges, researchers from Syrian institutes are still working on research projects.