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Aim This study aimed to assess anxiety and depression among health sciences students at home quarantine during the COVID-19 pandemic in selected provinces of Nepal. Methods A web-based cross-sectional study was conducted among 409 health science students enrolled at graduate and post-graduate levels in selected universities and their affiliated colleges. Students from selected colleges were asked to fill out a survey, that was made available through email and social media outlets such as Facebook and Viber. The data were downloaded in Ex