OBJECTIVES: To investigate levels of distress, depression, anxiety, stress and perception of their current study situation during the COVID-19 pandemic among undergraduate dental and medical students. DESIGN: Observational, cross-sectional study including two consecutive surveys (May and July 2020). SETTING: A large medical school in Germany. PARTICIPANTS: All first year dental and medical students were invited. 132 participating first year students (44 dental, 88 medical) from the first survey and 150 students (50 dental, 100 medical) from the second were included in our analyses. PRIMARY AND SECONDARY OUTCOME MEASURES: Mental burden (distress thermometer, Patient Health Questionnaire-4, Perceived Stress Scale-4) and self-reported changes in mental health and perception of study situation during the COVID-19 pandemic (self-developed items) were compared. Open-ended questions were analysed by conventional content analyses. RESULTS: A considerable proportion of students (t1: May 2020: 84.1%; t2: July 2020: 77.3%) reported distress levels above cut-off. In July 2020, dental students reported significantly higher distress scores than medical students (dental: M=7.0, SD=2.3; medical: M=5.7; SD=2.1; p<0.001). More dental than medical students reported mild, moderate and severe levels of anxiety and depression symptoms. The majority stated that their mental health and study motivation had not changed during the pandemic. Logistic regression showed that being a dental student was significantly associated with a higher likelihood for serious worries regarding the study situation during COVID-19 at t1 (OR 4.0; 95% CI 1.1 to 14.2). At t2 higher distress was significantly associated with a higher likelihood for experiencing serious worries (OR 1.8; 95% CI 1.3 to 2.5). Regarding current concerns related to the pandemic, students most frequently reported difficulties with self-regulated learning (15.2%), study-related worries and uncertainty (14.4%), missing feedback of students and lecturers (11.4%) and lack of practical training (9.8%). CONCLUSION: The results suggest that high mental burden and the lack of practical training among medical and dental students is an increasing problem, with a possibly even higher urgency in dental students. Tailored psychological and educational support offers during and after the COVID-19 pandemic might help them as they progress through (medical and) dental school.