The research portfolio of the Department of Public Health includes studies on all major aspects of health research, and these can be listed as following:

- longitudinal studies of the health of adolescents in international comparison
- health monitoring of a representative sample of the Estonian adult population;
- the epidemiology of HIV and sexually transmitted diseases in Estonia;
- efficacy of HIV prevention and treatment;
- evaluation of efficacy of health programmes and interventions;
- access and quality of medical care;
- health technology assessment;
- socio-economical determinants of health;
- health in working environment.

In 2008 the Department established Unit of Health Information Analysis, the aim of which is to support planning and decision-making with interdisciplinary research in disease epidemiology, health interventions and programmes, and in provision of health services.