OBJECTIVE To estimate the association between the intensity of animal infection with Schistosoma japonicum and human infection in Western Samar province, the Philippines. METHODS We conducted an observational cross-sectional study of 1425 households in 50 villages. Stool samples were collected on each of 1-3 days from 5623 humans, 1275 cats, 1189 dogs, 1899 pigs, 663 rats and 873 water buffalo. Intensity of infection with S. japonicum was measured by the number of eggs per gram (EPG). Egg counts were done using the Kato-Katz method. We used a Bayesian hierarchical cumulative logit model, with adjustments for age, sex, occupation and measurement error. RESULTS The adjusted proportions of humans lightly infected (classified as 1-100 EPG) was 17.7% (95% Bayesian credible interval = 15.3-20.2%); the proportion classified as at least moderately infected (>100 EPG) was 3.2% (2.2-4.6%). The crude parasitological results for animals indicated that 37 cats (2.9%), 228 dogs (19.2%), 39 pigs (2.1%), 199 rats (30.0%) and 28 water buffalo (3.2%) were infected. In univariate analyses the odds ratios corresponding to a unit increase in the mean number of EPG at the village-level in dogs was 1.05 (1.01-1.09), in cats 1.35 (1.02-1.78), in pigs 1.16 (0.24- 5.18) and in rats 1.00 (1.00-1.01). Mean EPG values in cats, dogs, pigs and rats were correlated with one another. This confounding made interpreting the odds ratios difficult, but the odds ratios for dogs and cats were more consistent. CONCLUSIONS S. japonicum is endemic in areas of the Philippines despite implementation of control programmes. This may be due to the association of infections in dogs and cats with human infections. Infection control in dogs and cats is challenging, and there is a need to develop new methods to control transmission across all species.