This nested case-control study investigated the risk factors for gastroenteritis in a cohort using rainwater as their primary domestic water source. Consumption of beef [odds ratio (OR) 2·74, 95% confidence interval (CI) 1·56–4·80], handling of raw fresh chicken in the household (OR 1·52, 95% CI 1·02–2·29) and animal contact (OR 1·83, 95% CI 1·20–2·83) were found to be significant risk factors (P>0·05). Significant protective effects were observed with raw salad prepared at home (OR 0·33, 95% CI 0·18–0·58), consumption of salami (OR 0·60, 95% CI 0·36–0·98), and shellfish (OR 0·31, 95% CI 0·14–0·67). This study provides novel insight into community-based endemic gastroenteritis showing that consumption of beef was associated with increased odds of illness and with a population attributable fraction (PAF) of 57·6%. Detecting such a high PAF for beef in a non-outbreak setting was unexpected.