Occlusal dental caries often is not apparent using traditional diagnostic techniques. The clinical significance of pit-and-fissure discoloration in the absence of dietary and habit substances was examined. The study included 462 extracted teeth (216 with obvious pit-and-fissure discoloration, 216 with subtle discoloration, and 30 with no discoloration); 130 clinical teeth with varying degrees of pit-and-fissure discoloration; and 159 teeth in young adults, which had sealants placed > or = 10 years. All teeth studied were excavated very conservatively using air abrasion and/or the uniquely small H1 004 carbide bur. Presence of caries and its depth and extent were recorded, photographed, and measured with a custom made calibrated probe. Of the 721 teeth with discolored pits and fissures studied (432 extracted teeth and 289 clinical teeth), 660 (92%) had two or more of the four clinical criteria used to define dental caries in this study. Sixty-four percent of the lesions were > 2 mm in depth and 27% were > 3 mm in depth. Of the 159 teeth sealed for > or = 10 years, 47 (92%) were carious, and 26% had large, deep carious lesions penetrating > 3 mm. These data indicate: more effective methods are needed to diagnose pit-and-fissure caries and presence of pit-and-fissure discoloration in the absence of substances causing extrinsic staining should be a strong warning for clinicians to examine carefully for dental caries.