Objective A recent report from a non-nationally representative, geographically diverse sample in four separate communities in Peru suggests an unusually high diabetes incidence. We aimed to estimate the national diabetes incidence rate using PERUDIAB, a probabilistic, national urban population-based longitudinal study. Research design and methods 662 subjects without diabetes, selected by multistage, cluster, random sampling of households, representing the 24 administrative and the 3 (coast, highlands and jungle) natural regions across the country, from both sexes, aged 25+ years at baseline, enrolled in 2010–2012, were followed for 3.8 years. New diabetes cases were defined as fasting blood glucose ≥126 mg/dL or on medical diabetes treatment. Results There were 49 cases of diabetes in 2408 personyears follow-up. The weighted cumulative incidence of diabetes was 7.2% while the weighted incidence rate was estimated at 19.5 (95% CI 13.9 to 28.3) new cases per 1000 person-years. Older age, obesity and technical or higher education were statistically associated with the incidence of diabetes. Conclusion Our results confirm that the incidence of diabetes in Peru is among the highest reported globally. The fast economic growth in the last 20 years, high overweight and obesity rates may have triggered this phenomenon.