The prevalence of Giardia and Cryptosporidium among 3,456 diarrheic patients corrected from May 2004 to May 2005 in the Philippines was determined. Of 133 (3.8%) positive samples, 69 (2.0%) were positive for Giardia and 67 (1.9%) for Cryptosporidium. Three samples had co-infection with Giardia and Cryptosporidium. Luzon had the highest positive samples (5.0%) followed by Mindanao (4.9%), then Visayas (2.2%). Giardia was most prevalent in Mindanao (3.6%) while Cryptosporidium was most prevalent in Luzon (3.1%). The prevalence of Giardia (2.0%) among pediatric patients (0-18 years) did not significantly differ from that (1.9%) among adults (> 18 years old). However, for Cryptosporidium, the prevalence (2.9%) among pediatric patients was significantly higher compared to that (0.2%) among adult patients. In the pediatric population, the highest percentage of patients with Giardia was the 5-9 year old age group, while that of Cryptosporidium was in the 0-4 year old group. The prevalence of Giardia, but not Cryptosporidium, was significantly higher in male than female adults. Seasonality had a distinct peak in September with Cryptosporidium more prevalent in the rainy (2.6%) than dry season (0.9%).