The purpose of this in vitro study was to assess the validity and reproducibility of the diagnosis of fissure caries prior to and following the placement of a clear sealant. One hundred and twelve extracted molar teeth were examined by 7 experienced clinicians. Each examiner conducted four visual examinations, 2 prior to and 2 after sealing, allowing an assessment of reproducibility. The teeth were subsequently serially sectioned to provide the histological validation. After placement of a sealant, a significant (p < 0.05) loss of sensitivity was found for the diagnosis of enamel lesions and dentine lesions, but specificity was not altered. The overall reproducibility expressed by the kappa statistic was 0.60 and 0.47, before and after sealing, respectively. The examiners significantly (p < 0.001) underestimated the severity of lesions detected after sealing compared to their assessment prior to sealing. The investigation suggests that sealed surfaces require careful assessment and monitoring.