Background A cross-sectional survey was performed in 2012 among 18 rural barangays in Northern Samar, the Philippines in order to determine the prevalence of single and multiple species helminth infections and the underlying risk factors of acquiring one or more parasites. Methods A total of 6976 participants who completed a medical questionnaire and provided a stool sample for examination were included in the final analysis. Results The overall prevalence rates of Schistosoma japonicum, Ascaris lumbricoides, Trichuris trichiura, and hookworm were found to be moderate to high at 28.9%, 36.5%, 61.8%, and 28.4%, respectively. However, the prevalence of harbouring any of the helminths was found to be higher at 75.6%. Significant variation was evident among the predicted barangay-specific random effects for infection with S. japonicum (barangay variance of 0.66, 95% confidence interval 0.31–1.40) and for any helminth infection (barangay variance of 0.63, 95% confidence interval 0.30–1.29). The predictive models showed, with greater than 80% sensitivity and specificity, that low socio-economic status, low levels of education, poor sanitation, proximity to water sources, occupation (i.e., farming and fishing), and male sex were all reliable indicators of infection status. Conclusions This study will aid in the targeting of limited resources for national treatment and WASH (water, sanitation, and hygiene) efforts in low- and middle-income countries.