Objectives Bioactive glasses which degrade in aqueous solutions may release bioactive ions such as fluoride (F - ) and support fluoride bioavailability in saliva. We investigated how these effects would be apparent in an in vivo experimental trial after toothbrushing in comparison with sodium fluoride and amine fluoride. Material and methods In this single-center, randomized, parallel in vivo trial with a three strata block design, where healthy subjects were randomly assigned into three groups. Each group brushed their teeth either with fluoridated bioactive glass containing dentifrice, with a sodium fluoride (NaF) containing dentifrice or with amine fluoride (AmF) containing toothpaste. Saliva was collected time intervals before, immediately after, 30, 60 and 120 min after toothbrushing. Fluoride concentration was determined in supernatant saliva and salivary sediment using a fluoride ion selective electrode. The data were evaluated statistically using non-parametric tests. Results The increase of bioactive fluoride in supernatant saliva was higher after application of NaF or AmF compared to fluoridated bioactive glass. In salivary sediment bioavailability of fluoride lasted longer after application of fluoridated bioactive glass. Conclusions Toothbrushing with the fluoride containing bioactive glass dentifrices had positive effects on the fluoride bioavailability within two hours. Fluoride containing bioactive glass represent a new area for investigation in caries prophylaxis. The bioactive potential impact on the tooth remineralization should be examined further. Trial registration DRKS00016038 .