The aim of this study was to assess the reliability of three diagnostic methods (near-infrared transillumination (NIRT), bitewing radiographs (BW), and clinical images (CI)) to detect occlusal carious lesions in a low caries risk population. This retrospective analysis included one hundred and eighty-eight occlusal surfaces, scored as sound surface, early lesion, or distinct lesion. We evaluated the agreement between and within the methods over time. Kappa statistics tested the correlation between the methods. Examiners detected occlusal early lesions more frequently with visual examination and NIRT and the same lesions were confirmed on the 2-year follow-up. Within the limitations of this study, we were able to establish that early occlusal lesions can be detected and monitored over time using NIRT and visual exam, while BW scores showed mostly sound surfaces at both examinations. NIRT combined with clinical examination can be considered appropriate to detect and monitor early enamel caries on the occlusal surface in low caries-risk populations.