Billions of people had to face self-isolation for several months due to COVID-19 pandemic; given that, it seems quite vital to provide theoretical grounds for sanitary-hygienic health risk assessment. Our research objects were people who had to self-isolate during CIVID-19 pandemic. In our research we provided theoretical substantiation for priority health risk factors determined by hypodynamia, hypoxia, improper nutrition, distorted work and leisure regime, and psychoemotional strain. These factors can result in growing morbidity with non-communicable diseases among population. Our research goal was to give theoretical grounds for sanitary-hygienic assessment of health risk factors caused by self-isolation, to reveal priority health risk factors causing morbidity with non-communicable diseases, and to give recommendations on how to prevent it. We applied analytical, information, and statistical procedures in our research. Data were obtained from regulatory and legal documents on sanitary-hygienic standardization in the Russian Federation, specifically, data on nutrition hygiene, occupational hygiene, children and teenagers hygiene, etc.; we also revised scientific works published by Russian and foreign authors and analyzed documents issued by the World Health Organization as well as by public healthcare authorities in different countries during COVID-19 pandemic. When developing theoretical grounds for sanitary-hygienic assessment of health risk factors causing morbidity with non-communicable diseases due to self-isolation, we determined priority risk factors and suggested certain hygienic criteria for assessing self-isolation. We provided theoretical substantiation for a suggested hygienic self-isolation index and its score estimate. The existing system for sanitary-hygienic standardization in the RF fixes requirements for nutrition, work, and leisure regime as well as people’s physical activity; it was applied for performing hygienic assessment of self-isolation and self-isolation index score estimates. We suggested certain activities aimed at minimizing health risks under self-isolation; these activities were based on sanitary-hygienic standards. Since hypodynamia and hypoxia are primary sanitary-hygienic health risk factors, we suggest sticking to adequate nutrition with optimal energy capacity, proper physical activity, as well as proper work and leisure regimes.