In the face of limited health resources, there is an increasing need for evidence-based priority-setting health program and economic evaluations. This has led to a demand for enhanced knowledge about the relative contributions of specific diseases and injuries to the loss of healthy life. Public Health Ontario (PHO) and the Institute for Clinical Evaluative Sciences (ICES) conducted a study to estimate the burden of infectious diseases in Ontario. Using health-adjusted life years, a composite health gap measure that allows for the simultaneous description of both mortality and morbidity, the study estimated the disease burden of 51 infectious disease agents. Data sources included census estimates, vital statistics, public health reportable disease data, health-care utilization data, cancer registries and epidemiological studies. Results indicate that each year in Ontario, over 7,000,000 infectious disease episodes and nearly 4,900 deaths occur from infectious diseases. For most infectious diseases, mortality contributes more to disease burden than reduced functioning. Out of the infectious disease agents studied, the most burdensome are: hepatitis C virus (HCV), Streptococcus pneumoniae, human papillomavirus (HPV), hepatitis B virus (HBV), Escherichia coli, HIV/AIDS, Staphylococcus aureus, influenza, Clostridium difficile, and rhinovirus. Although the overall burden is similar between males and females, marked differences in sex-specific burden are notable for certain pathogens (i.e., HCV, HBV, HPV, HIV/AIDS) and syndromes (e.g. urinary tract infections).