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Background There is a global trend of increasing use in prescription and over-the-counter (OTC) drugs. This hasn’t been verified in Canada. In addition, there are changes made to the collection method of medication information after the Canadian Health Measures Survey (CHMS) cycle 2. This study aims to review the potential impact of the changes in medication data collection and the trends in medication use if data quality remains similar throughout the CHMS cycles 1 to 4. This is fundamental for the analysis of this biomonitoring database. Methods The CHMS cycle 1 to 4 medication and household data were used to study the trends of medication use between 2007 and 2015. The use of prescription or OTC drugs was grouped based on the first levels of the Anatomical Therapeutic Chemical (ATC) Classification system. The total numbers of medications were asked in all cycles. However, only a maximum of 15 and 5 drugs could be respectively reported for existing and new prescription or OTC drugs in cycles 1 and 2. There were no restrictions on drug reporting after cycle 2. The trends of medication use were described as ratios, compared to cycle 1. Results The total numbers of the types of medication ever identified decreased from 739 to 603 between cycles 1 and 4. The proportions of using any drugs were from 0.90 to 0.88 between cycles 1 and 4 (ratio = 1.08 in cycle 4, 95% CI = 0.89 to 1.26). The numbers of drugs in use were from 3.9 to 3.8 (ratio = 1.05 in cycle 4, 95% CI = 0.86 to 1.24). The proportions of prescription drug use were from 0.53 to 0.55 (ratio = 1.13 in cycle 4, 95% CI = 0.89 to 1.37), while the numbers of prescription were from 1.51 to 1.68 (ratio = 1.20 in cycle 4, 95% CI = 0.92 to 1.48). The use of diabetes and thyroid medication had trends similar to the respective disease prevalence. The use and the numbers of drugs for blood and blood forming organs significantly increased between cycles 1 and 4 (ratio = 1.56 in cycle 4, 95% CI = 1.03 to 2.10). Conclusions There is an increasing trend in the use of blood and blood forming agents through cycles 2 to 4 and cardiovascular drugs in cycle 3. For diabetes and thyroid medication, the proportions of medication use increase proportionally with disease prevalence. The changes in the medication information collection method may not have important impact on the reporting of the use of prescription or OTC drugs.