OBJECTIVE: To longitudinally apply a laser fluorescence (LF) device (DIAGNOdent) in newly erupted 1st permanent molars over a 3-year period and to relate the findings to mutans streptococci (MS) colonization, fissure morphology, and caries development. MATERIAL AND METHODS: The material consisted of 101 consecutive 5 to 6-year-old children attending a Public Dental Clinic and who volunteered after ethical approval and informed consent had been given. Only fully erupted molars with clinically sound fissures were included. At baseline, the fissures were subjectively categorized as "shallow" or "deep", and, prior to the LF readings, a plaque sample was collected and cultivated for MS using a chair-side kit. The registrations were repeated annually and the microbial samplings after 2 years. The total drop-out rate was 12%. RESULTS: The mean LF values increased significantly (p<0.05) with increasing age from 8.2 to 12.4 in the teeth that remained sound. Thirty-five teeth were decayed or filled during the follow-up and their mean LF values increased from 13.4 to 40.7. The LF readings were significantly higher in molars with "deep" fissures (p<0.05) at all visits. MS colonization at baseline was associated with an increased risk for caries (OR = 11.6, p<0.05) and significantly elevated LF readings. Baseline LF readings > or =12 were not diagnostic for dentin caries or fillings over the study period (sensitivity 0.57; specificity 0.86). CONCLUSION: LF readings could be used to some extent to monitor fissure morphology and caries development in fissures of newly permanent molars over time, but elevated initial values were not predictive for caries development.