This study was designed to evaluate the effectiveness of a WHO-supervised school based preventive program for Filipino children. 19 primary schools in deprived communities of rural areas in Northern Mindanao had been selected to take part in the program. By using WHO criteria (1997) one dentist examined 1574 children with an mean age of 7.1 years. The percentage of caries free children was 8.8. Caries prevalence was 1.2 DMFT (± 1.4) and 7.2 dmft (± 5.1). Fillings were not recorded in both dentitions. The mt value was 0.2 (+ 0.7). The preventive program focused on preventive (dietary control, supervised toothbrushing with a fluoridated toothpaste, professional application of fluoride varnish). In order to cope with the high treatment need invasive measures (extractions of deciduous teeth, ART-fillings in permanent teeth) had to be included too. 1162 children with a mean age of 10.2 years were re-examined after three years. The percentage of caries free children was 16.2. Caries prevalence of 1.6 DMFT (± 1.8) was distributed to 0.5 DT, 0.2 MT and 0.9 FT component. The increment of 0.4 DMFT and the distribution of the DMFT components in high caries risk Filipino children reflect the effectiveness of a comprehensive dental care approach. Extractions of carious deciduous teeth and ART-restorations in permanent teeth might be an important impact for reducing the microbial infection in the oral cavity. We conclude that invasive measures seem to be a prerequisite for the caries preventive effect of daily toothbrushing with fluoridated toothpaste in children with high caries experience, particularly in the mixed dentition. Keywords: caries prevalence, Philippine, preventive programme