Objectives: The aim of this study was to assess the prevalence of black stain to the caries experience among Filipino children living in rural areas of Northern Mindanao/ Philippines. Methods: A total of 1764 sixth graders with a mean age of 11.5 ± 1.3 years were clinically examined according to the WHO standard for oral health surveys (1997) by 11 calibrated dentists. Presence and absence of black stain was recorded. DMFT was calculated (SPSS, version 11.05) and comparisons in the group of children with and without black stain were made (Mann-Whitney U and chi square test; á = 0.05). The kappa value of 0.92 was calculated for the inter-examiner reproducibility. Results: Black stain was observed in 15.9% of the population (n = 281). The percentage of caries-free children was significantly higher in children with black stain (47.0%) than in children without black stain (24.5%). Children with black stain had a significantly lower DMFT (1.6 ± 2.2) compared to 2.2 ± 2.6 DMFT in children without black stain. The mean number of initial caries lesions located on occlusal surfaces of the first molars (brown and white discoloured fissures) and on smooth surfaces (white spots) of the central upper and lower incisor (11, 31) was not different between both groups (1.5 ± 1.4 vs 1.2 ± 1.4). In 4 schools, all located in very poor, remote areas, 50.4% of the students revealed black stain with 0.8 ± 1.2 DMFT. Among these children 53.4% were caries-free. Children without black stain had a DMFT of 1.7 ± 1.8 and the percentage of caries-free children was 40.4%. Conclusion: Further studies are of interest to examine the microflora and the diet behaviour of children with black stain especially among those living in remote areas with a high frequency of this plaque type.