This study aimed to establish the relationship between the prevalence of active trachoma in children, water availability and household water use in a village in Tanzania. Nine hundred and fourteen children aged 1-9 years were examined for signs of trachoma. Data were collected on time taken to collect water, amount of water collected and other trachoma risk factors. In a sub-study, 99 randomly selected households were visited twice daily on two consecutive days to document patterns of water use. The prevalence of active trachoma in the children examined was 18.4% (95% CI 15.9-20.9). Active trachoma prevalence increased with increasing water collection time (OR 2.25; 95% CI 1.13-4.46) but was unrelated to the amount of water collected. In the sub-study, active trachoma prevalence was substantially lower in children from households where more water was used for personal hygiene (P for trend < or =0.01), independent of the total amount of water used. The allocation of water to hygiene was predicted by lower water collection time. The key element in the relationship between water availability and trachoma is the allocation of water within households. Collection time may influence both the quantity of water collected and its allocation within the household.