Introduction: The Public Health Agency of Canada’s Canadian Chronic Disease Surveillance System (CCDSS) uses a validated, standardized methodology to estimate prevalence of individual chronic diseases, such as diabetes. Expansion of the CCDSS for surveillance of multimorbidity, the co-occurrence of two or more chronic diseases, could better inform health promotion and disease prevention. The objective of this study was to assess the feasibility of using the CCDSS to estimate multimorbidity prevalence. Methods: We used administrative health data from seven provinces and three territories and five validated chronic conditions (i.e. cardiovascular disease, respiratory disease, mental illness, hypertension and diabetes) to estimate multimorbidity prevalence. We produced age-standardized (using Canada’s 1991 population) and age-specific estimates for two multimorbidity definitions: (1) two or more conditions, and (2) three or more conditions from the five validated conditions, by sex, fiscal year and geography. Results: Among Canadians aged 40 years and over in the fiscal year 2011/12, the prevalence of two or more and three or more chronic conditions was 26.5% and 10.2%, respectively, which is comparable to other estimates based on administrative health data. The increase in multimorbidity prevalence with increasing age was similar across provinces. The difference in prevalence for males and females varied by province and territory. We observed substantial variation in estimates over time. Results were consistent for the two definitions of multimorbidity. Conclusion: The CCDSS methodology can produce comparative estimates of multimorbidity prevalence across provinces and territories, but there are challenges in using it to estimate temporal trends. Further expansion of the CCDSS in the number and breadth of validated case definitions will improve the accuracy of multimorbidity surveillance for the Canadian population.