Experimental studies have demonstrated that mutans streptococci play a major role in caries etiology. Several previous epidemiologic studies found a positive association of salivary mutans streptococci with caries prevalence. The present epidemiologic study aimed at detecting a possible association of salivary mutans streptococci with brown discoloured pits and fissures, supposing that discolouration indicates caries. In the Canton of Zurich 1035 schoolchildren, aged 6.5-12.5, were examined with regard to caries prevalence and presence of discolourations in pits and fissures. A commercially available, semi-quantitative test was used to estimate the salivary level of mutans streptococci in each child. The salivary level (low/high) of mutans streptococci was significantly associated with the presence of slightly brown discoloured (C1), clearly brown discoloured (C2) and cavitated (C3) pits and fissures. The odds ratios were 1.5 (P<0.01) for C1, 2.5 (P<0.001) for C2 and 5.0 (P<0.001) for C3 pits and fissures. The findings are consistent with the hypothesis that brown discolouration indicates caries. Furthermore, the findings suggest that this type of discolouration at elementary school age indicates increased caries activity.