OBJECTIVES: To determine the prevalence of obesity indices (body mass index (BMI), waist circumference (WC), body fat per cent (BF%)) and cardiometabolic risk factors. To investigate the association between obesity indices and cardiometabolic risk factors in a Zanzibari population. DESIGNS:Cross-sectional study. SETTINGS: Participants randomly selected from 80 Shehias (wards) in Unguja, Zanzibar in 2013. PARTICIPANTS: A total of 470 participants between 5 and 95 years were examined. Data on socioeconomic status, area of residence, anthropometry and venous blood were collected. Associations between obesity indices and cardiometabolic risk factors were investigated using multilevel logistic regression analyses in two steps: first, each obesity indicator was tested independently; second, all indicators combined in one model were tested for their association with cardiometabolic risk factors. RESULTS: The proportion of overweight/obese individuals was 26.4%, high WC (24.9%) and high BF% (31.1%). Cardiometabolic risk factors with highest prevalence of abnormal values included hypertension (24.5%), low high-density lipoprotein cholesterol (HDL-C) (29.4%), high low-density lipoprotein cholesterol (LDL-C) (21.3%) and high glycated haemoglobin (HbA1c) (19.1%). Obesity and hypertension increased with age, and were most prevalent in participants aged 45 years and above. Low HDL-C was most prevalent among participants aged ≥18 to <45 years, while high LDL-C was more prevalent in those above 45 years. High WC and high BF% were associated with high levels of LDL-C (OR=2.52 (95% CI 1.24 to 5.13), OR=1.91 (95% CI 1.02 to 3.58), respectively). Additionally, BMI and WC were associated with high levels of HbA1c (OR=2.08 (95% CI 1.15 to 3.79), OR=3.01 (95% CI 1.51 to 6.03), respectively). In the combined regression model, WC was associated with higher chances for hypertension (OR=2.62 (95% CI 1.14 to 6.06)) and for high levels of HbA1c (OR=2.62 (95% CI 1.12 to 6.15)). CONCLUSION: High BMI, WC and BF% were strongly associated with hypertension, with individuals with high WC being twice more likely to have hypertension; this calls for early and effective screening strategies for this study population.