To compare the penetration and the imperviousness of two pit and fissure sealants according to surface treatments involving different cleaning procedures with or without subsequent acid etching. Two sealants were used: a resin-based sealant (Concise White Sealant) and a compomer-based material (Dyract Seal) coupled with an enamel-dentin bonding agent (Dyract Seal and Prime&Bond NT). Extracted molars (n = 120) were randomly divided into 12 groups: 4 control and 8 experimental groups that received different surface treatments. Pumice, alumina, or bicarbonate was used to clean the surfaces. Phosphoric acid or non-rinse conditioner was used as acid etching agents. After sealing, the Concise White Sealant groups were directly thermocycled for 1800 cycles, while the Dyract Seal groups were stored in water for one month before thermocycling. After apex sealing and varnish coating, the fillings were stained with silver nitrate and embedded. Three to 6 cross sections of 200 µm each were made per sample to assess both sealant penetration (% of the length of the fissure) and the imperviousness of the seal (scores method). Concise White Sealant achieves a better enamel sealing than Dyract Seal when the teeth are treated with air abrasion or air polishing followed by etching. Acid etching is essential for good sealing, whatever the material and cleaning technique tested. Only the combination of air abrasion and phosphoric acid etching yielded a leak-free joint. This study clearly shows that penetration and sealing are two different phenomena. Ideally, an efficient sealant must have a good sealing ability and a high rate of infiltration as well, but these two properties probably do not have the same clinical relevance. The imperviousness of the seal remains the most important requirement.