Background: The aim of this study is to evaluate the clinical success of different fissure sealants applied to erupting permanent first molars by taking into consideration the stages of tooth eruption. Materials and Methods: Two hundred healthy children between ages 5 and 8 with the inclusion criteria were examined. The erupting permanent first molars were evaluated and those at stage 3 or 4 were selected. An investigator placed three different fissure sealants (giomer, hydrophilic, and hydrophobic resin-based). At the end of 18 months, retention loss, development of new dental caries, localization of retention losses, marginal integrity, and marginal discoloration were evaluated. Results: The rate of tooth with total retention at stage 3 was significantly higher (P < 0.05). The development of dental caries in teeth at stage 4 was found to be significantly higher than that of stage 3 (P < 0.05). In terms of marginal integrity, the difference between stages of tooth eruption is similar (P > 0.05). Regarding marginal discoloration, fissure sealants applied at stage 3 were considered to be more successful than those applied at stage 4 (P < 0.05). Conclusions: We may conclude that the tooth eruption affects clinical success and giomer-based fissure sealants may not be an alternative for resin-based fissure sealants in erupting teeth.