The first two phases of a national prevalence survey of schistosomiasis in The Philippines were completed in Mindanao in 2005 and the Visayas in the first quarter of 2007. The design was a stratified two-step systematic cluster sampling, with two Kato-Katz thick smears examined from each participant. In Mindanao, a total of 22 provinces spread in six regions were covered by the survey with five barangays (equivalent to a village) per province for a total of 110 barangays. The response rate was 70.9% with a total of 21,390 individuals examined. The province of Maguindanao, a known endemic area for schistosomiasis japonica, failed to take part in the survey. In the Visayas, 10 out of 11 provinces, spread out in three regions, participated in the survey. There were 6321 respondents for an overall participation rate of 32.2%. Mindanao showed a wider coverage of the disease than the Visayas (60% versus 45%). By region, Caraga or Region 13 ranked first in Mindanao and Region 8 in the Visayas. By province, Agusan del Sur is first on the list, followed by Northern Samar and then Eastern Samar. Overall, the prevalence rate among males is higher than that of females suggesting the occupational hazard of farming and fishing among the males. The higher exposure among farmers and fishermen is also borne out by the age distribution of the disease. Prevalence remains consistently high among the adults compared with the younger age groups. The survey also covered other helminth infections that can be detected in a stool survey, notably soil-transmitted helminthes and food-borne trematodes.