The Canadian Index of Wellbeing (CIW) is an ambitious undertaking that aims to measure and track Canadians' overall "wellbeing". The Healthy Populations, one of eight CIW domains, brings together both population health outcomes and important influences on health. Indicators from eight subdomains (personal wellbeing, life expectancy/mortality, physical health conditions, functional health, mental health, lifestyle and behaviour, health care, and public health) make up the Healthy Populations domain. Following a review of worldwide literature on health and wellbeing indicators, application of a prespecified set of selection criteria, and expert external validation, ten core indicators and six secondary indicators were selected. The data sources include several national population data systems (CCHS, NPHS) and databases kept at the Canadian Institute for Health Information. Indicators were examined for trends over time, and were stratified by age, sex, income and education. A single summary measure, health domain index, was calculated and reported annually from 1994 to 2008. Analysis of data over a 15-year time period found that Canadians are living longer, but with fewer years in optimal health. Diabetes rates have risen, along with obesity rates, while smoking rates are on the decline and regular physical activity is becoming more common. There were notable income and education gradients for virtually all indicators measured, and gender disparities evident for life expectancy, health-adjusted life expectancy, diabetes, and depression. A worrisome downward trend in health outcomes for Canada's youth (12-19 years) was observed. The overall health index score showed a modest rise of 6.6% from 1994 to 2008. The Healthy Populations domain, and its ongoing use and refinement, can be an important resource for understanding and monitoring the health of Canadians. Knowledge about the status of Canadians' wellbeing will benefit from the contextualization of these findings through evidence generated from the other CIW domains.