The aim of this study is to clinically analyse efficacy of detection of fissure caries with laser fluorescence method (DIAGNOdent) on different locations of the fissure system. Occlusal surfaces of 123 permanent molars were analysed with DIAGNOdent device on five different locations in the fissure system ; mesial, central, distal, oral and buccal fissure. A total of 579 different fissures of the occlusal surfaces were examined with DIAGNOdent device according to caries score: 0– 20 no caries, 21–99 caries. The fissures were opened (PFO) with Komet Micropreparation set No. 4377 burs and analysed with the following caries scores: 0 – no caries, 1 – enamel caries, 2 – dentin caries. From the total of 579 analysed fissures, 323 (55.8%) did not have any caries, 166 (28.7%) had enamel caries and 90 (15.5%) had dentine caries. The specificity (SP) and sensitivity (SE) of DIAGNOdent for different fissures is as follows: mesial 0.93 (SP) 0.71 (SE), central 0.85 (SP) 0.92 (SE), distal 0.92 (SP) 0.96 (SE), buccal 0.83 (SE) 0.92 (SE) and oral 0.88 (SE) 0.97 (SP). The overall SP and SE for DIAGNOdent was 0.88 and 0.92. Positive predictive value of DIAGNOdent device in different fissures is as follows: distal 96.3%, central 88.7%, oral 84.3%, mesial 78.5% and finally buccal 66.7%, the latter being statistically different from other fissures (chi square test, d.f. = 4, p ! 0, 001). According to PFO, enamel caries occurs most frequently in distal fissure (43.9%) and dentine caries in central fissure (23.5%) and that is statistically significant (chi square, d.f. = 8, p = 0.001). DIAGNOdent device showed a high degree of accuracy in analysis of occlusal fissure system which enables the precise analysis of different parts of that system and therapy by the principles of minimally invasive preparation.