OBJECTIVE: To determine the association between excess body fat, assessed by skinfold thickness, and the incidence of type 2 diabetes mellitus (T2DM) and hypertension (HT). DESIGN: Data from the ongoing PERU MIGRANT Study were analysed. The outcomes were T2DM and HT, and the exposure was skinfold thickness measured in bicipital, tricipital, subscapular and suprailiac areas. The Durnin-Womersley formula and SIRI equation were used for body fat percentage estimation. Risk ratios and population attributable fractions (PAF) were calculated using Poisson regression. SETTING: Rural (Ayacucho) and urban shantytown district (San Juan de Miraflores, Lima) in Peru. PARTICIPANTS: Adults (n 988) aged ≥30 years (rural, rural-to-urban migrants, urban) completed the baseline study. A total of 785 and 690 were included in T2DM and HT incidence analysis, respectively. RESULTS: At baseline, age mean was 48·0 (sd 12·0) years and 47 % were males. For T2DM, in 7·6 (sd 1·3) years, sixty-one new cases were identified, overall incidence of 1·0 (95 % CI 0·8, 1·3) per 100 person-years. Bicipital and subscapular skinfolds were associated with 2·8-fold and 6·4-fold risk of developing T2DM. On the other hand, in 6·5 (sd 2·5) years, overall incidence of HT was 2·6 (95 % CI 2·2, 3·1) per 100 person-years. Subscapular and overall fat obesity were associated with 2·4- and 2·9-fold risk for developing HT. The PAF for subscapular skinfold was 73·6 and 39·2 % for T2DM and HT, respectively. CONCLUSIONS: We found a strong association between subscapular skinfold thickness and developing T2DM and HT. Skinfold assessment can be a laboratory-free strategy to identify high-risk HT and T2DM cases.