We conducted a systematic review and meta-analysis to clarify the association between adiposity, diabetes, and physical activity and the risk of kidney stones. PubMed and Embase were searched up to April 22nd 2018 for relevant studies. Summary relative risks (RRs) and 95% confidence intervals (CIs) were calculated using random effects models. Thirteen cohort studies were included. The summary relative risk was 1.21 (95% CI 1.12–1.30, I2 = 76%, n = 8) per 5 unit increment in BMI, 1.16 (95% CI 1.12–1.19, I2 = 0%, n = 5) per 10 cm increase in waist circumference, 1.06 (95% CI 1.04–1.08, I2 = 67%, n = 3) per 5 kg increase in weight and 1.12 (95% CI 1.06–1.18, I2 = 86%, n = 3) per 5 kg of weight gain. The summary RR was 1.16 (95% CI 1.03–1.31, I2 = 51%, n = 10) for participants with diabetes compared to participants without diabetes, and 0.93 (95% CI 0.78–1.10, I2 = 80%, n = 4) for high vs. low physical activity. These results suggest a positive association between adiposity and diabetes and the risk of kidney stones, but no association with physical activity.Electronic supplementary materialThe online version of this article (10.1007/s10654-018-0426-4) contains supplementary material, which is available to authorized users.