This in vivo study aimed to evaluate the performance of 2 fluorescence-based methods in detecting occlusal caries lesions in primary teeth, compared with the performance of visual inspection and radiographic methods, and to propose a mathematic correction of the diagnostic parameters due to the imperfect reference standard method used in the study. Two examiners assessed the occlusal surfaces of 407 primary teeth (62 children) using visual inspection (ICDAS), radiographic, DIAGNOdent pen (pen type laser fluorescence; LFpen), and fluorescence camera (FC) methods. At the noncavitated threshold (NC) the reference standard method was the results of ICDAS, and at the dentine caries threshold (D3) teeth diagnosed with dentine caries by ICDAS or radiographic methods were subjected to operative treatment to confirm the presence of lesion. Reproducibility, sensitivity, specificity, accuracy, and the area under the ROC curve were calculated for the methods at both thresholds. At the NC threshold, LFpen had a slightly better performance compared to the FC and radiographic methods. However, at the D3 threshold, both fluorescence-based methods performed similarly. Visual inspection and radiographic methods presented higher specificities but lower sensitivities than fluorescence methods. After corrections, there was a significant decrease in some parameters. In conclusion, both fluorescence-based methods presented similar performance in detecting occlusal dentine caries lesions in primary teeth, but they usually gave more false-positive results than did the visual and radiographic methods. The correction proposed shows that the performance of the methods can be overestimated, and the correction should be validated and considered in further studies that use an imprecise reference standard method.