Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Carbonic anhydrase VI is a secreted enzyme that catalyzes the hydration of carbon hydroxide in saliva and other body fluids. This enzyme has been implicated in taste and gastrointestinal dysfunctions, tooth erosion, and caries. The purpose of this study was to analyze the allele and genotype distribution of three polymorphisms in the coding sequences of (CA6) gene and check for possible associations with salivary buffer capacity, number of decayed, missing, and filled teeth in deciduous and permanent teeth (dmft/DMFT, Decayed/Missing/Filled Teeth), plaque index (PI), and the plaque pH variation (Delta pH) in children aged 7-9 years. Two hundred and forty-five children from both genders, residents in area with fluoridated water (Piracicaba, Sao Paulo, Brazil) were divided into two groups: caries free and with caries. The clinical examinations were conducted by a single previously calibrated examiner (kappa = 0.91) in an outdoor setting using a mirror and a probe, according to WHO criteria index (dmft/DMFT). Approximately 2 h after the first daily meal, the buffer capacity (BC) and the plaque pH were analyzed by means of a pH meter and an ion selective electrode. Plaque pH was measured immediately and 5 min after a mouth rinse with a 10% sucrose solution. The data were submitted to chi(2), Student's, and Mann-Whitney tests (alpha = 0.05). The PI and Delta pH of the upper and lower teeth were significantly higher in the carious group than control (P<0.05). There was no difference between the groups in relation to BC. There was no association between the alleles and genotypes distributions for polymorphisms in the CA6 gene exons 2 and 3 and caries experience (P>0.05). There was a positive association between buffer capacity and the rs2274327 (C/T) polymorphism. The allele T and genotype TT were significantly less frequent in individuals with the highest buffer capacity (P = 0.023 and 0.045, respectively). This finding encourages future studies relating CA6 gene polymorphisms and their association with malfunctions, such as taste and gastrointestinal alterations, or the differential effect of chemical modulators on the protein products originated from the distinct genotypes of the CA6 gene. The Pharmacogenomics Journal (2010) 10, 114-119; doi:10.1038/tpj.2009.37; published online 1 September 2009102114119Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)CAPES [0120/05-7]FAPESP [05/57649-2]