The aim of the present study was to compare indirect methods to assess the clinical performance of pit and fissure sealants and validate the use of 3D scanners. Sample consisted of 58 plaster models of upper and lower first permanent molars, sealed with resin sealants, as well as photographs obtained during the 18-month follow-up. Pre-established criteria were applied to categorize the sealant presence/absence and marginal integrity. Two calibrated examiners performed the evaluations, independently, using Scanning Electron Microscopy (SEM; gold-standard), Photography, 3D (CEREC In Lab) and Stereomicroscope analysis. The intra-examiner Spearman correlation was 94% e 97%, respectively, and the inter-examiner was 96%. Data was submitted to Kappa test, Spearman correlation and Receiver Operating Characteristic Curve (ROC). 3D and SEM presented good concordance; Stereomicroscope showed regular concordance with SEM and 3D (p<0.001). There was no concordance among Photography and the other methods (p>0.05). SEM had a significant positive correlation with 3D and Stereomicroscope (r=0.76 and 0.71, respectively; p<0.01). There was significant positive correlation (r=0.65) between 3D and Stereomicroscope (p<0.01). The ROC estimated curve areas for Stereomicroscope and 3D were 0.90 (IC:0.81-0.99) and 1.0 (IC:1.0-1.0), respectively (p<0.001). Photography presented lower sensitivity and specificity (area=0.59). 3D method showed the best performance when compared to gold standard, exhibiting high sensitivity and specificity, therefore, it was validated as a reliable method to evaluate pit and fissure sealants.