Introduction Syria has been suffering war for 10 years and COVID-19 added particular stress to people. Medical students are more prone than general population to anxiety and obsessive-compulsive disorder (OCD) which we are going to assess in this study. Methods This is a cross-section study that used online questionnaires were distributed in Social Media groups that included medical students. They included demographics, Zung self-Rating Anxiety Scale (SAS) and Yale-Brown OCD Scale (YBCOS). Results Overall, 180 participants were included, of which, 67 (37.2%) were males. Females and interns had higher OCD scores compared with males and more junior students p<0.05. OCD scores were not associated with social status, work, smoking, residency status, or having chronic diseases. Factors that were associated with higher anxiety scores were female gender and smoking p<0.05. In contrast, anxiety had no significant association with social status, residence status, academic year, work, and chronic diseases. Anxiety scores were not correlated with the consumption of tea, coffee, mate, or alcohol. OCD scores were also not correlated with coffee, mate, or alcohol consumption, but they were significantly correlated with tea consumption. When using regression, OCD and anxiety were associated with only sex, smoking and with each other. Conclusion These numbers were not higher than most of other studies. Further studies are needed for further evaluation to determine the cause whether it was from war having equal effect on mental health or COVID did not affect people as much in Syria.