In this prospective, double-blind, split-mouth-designed study, sealant retention rate and quality of two light-cured, fluoride-releasing sealants (Helioseal F, Fissurit F) were compared. Additionally the influence of the isolation method was evaluated. Fifty-eight subjects participated; 1 year later 54 of these (mean age 13.7 +/- 3.6 years) were reexamined. Sealants were applied to 203 tooth pairs (168 conventional and 25 invasive sealants). After 1 year, 193 tooth pairs were available for study; 82 were applied using rubber dam and 111 using cotton roll isolation. Retention rate and sealant quality were judged clinically and with photographs. The initial sealant quality was comparable for both materials. After 1 year, 53.4% of the Helioseal F sealants (44.6% of the Fissurit F sealants) were fully intact, 43.1% (51.8%) partially intact and 3.6% (3.6%) completely lost (P < 0.001). Placement under rubber dam resulted in significantly higher retention rates for both sealants (P < 0.001) as well as in an improved sealant quality. Cases of complete loss only occurred in teeth isolated with cotton rolls. The findings suggest that placement under rubber dam increases retention rate and sealant quality and may reduce material dependent factors that are considered a cause of sealant failures.