BACKGROUND: Studies have reported the incidence/risk of becoming obese, but few have described the trajectories of body mass index (BMI) and waist circumference (WC) over time, especially in low/middle-income countries. We assessed the trajectories of BMI and WC according to sex in four sites in Peru. METHODS: Data from the population-based CRONICAS Cohort Study were analysed. We fitted a population-averaged model by using generalised estimating equations. The outcomes of interest, with three data points over time, were BMI and WC. The exposure variable was the factorial interaction between time and study site. RESULTS: At baseline mean age was 55.7 years (SD: 12.7) and 51.6% were women. Mean follow-up time was 2.5 years (SD: 0.4). Over time and across sites, BMI and WC increased linearly. The less urbanised sites showed a faster increase than more urbanised sites, and this was also observed after sex stratification. Overall, the fastest increase was found for WC compared with BMI. Compared with Lima, the fastest increase in WC was in rural Puno (coefficient=0.73, P<0.001), followed by urban Puno (coefficient=0.59, P=0.001) and Tumbes (coefficient=0.22, P=0.088). CONCLUSIONS: There was a linear increase in BMI and WC across study sites, with the greatest increase in less urbanised areas. The ongoing urbanisation process, common to Peru and other low/middle-income countries, is accompanied by different trajectories of increasing obesity-related markers.