For the first time in the country, a national baseline prevalence survey using a well-defined sampling design such as a stratified two-step systematic cluster sampling was conducted in 2005 to 2008. The purpose of the survey was to stratify the provinces according to prevalence of schistosomiasis such as high, moderate, and low prevalence which in turn would be used as basis for the intervention program to be implemented. The national survey was divided into four phases. Results of the first two phases conducted in Mindanao and the Visayas were published in 2008. Data from the last two phases showed three provinces with prevalence rates higher than endemic provinces surveyed in the first two phases thus changing the overall ranking of endemic provinces at the national level. Age and sex distribution of schistosomiasis remained the same in Luzon and Maguindanao. Soil-transmitted and food-borne helminthes were also recorded in these surveys. This paper deals with the results of the last 2 phases done in Luzon and Maguindanao and integrates all four phases in the discussion.