The aim of the study was to evaluate possible long-term effects of a cereal diet supplemented with Lactobacillus paracasei F19 (LF19) during weaning on caries experience, mutans streptococci (MS) and lactobacilli (LBC) in a group of 9-year-old children. A secondary aim was to evaluate if the intervention resulted in the permanent integration of LF19 as part of the oral microbiota. The study followed up on a double-blind placebo-controlled randomised trial. Among 179 infants that were randomised to a daily diet that included cereals with or without LF19 from 4 to 13 months of age, 56 from the probiotic group and 62 from the placebo group participated in the follow-up at 9 years. Data were collected by oral clinical examination and questionnaires. MS and LBC levels were assessed with conventional cultivation; LF19 was detected by using randomly amplified polymerase chain reactions (RAPD-PCR). At the follow-up, neither decayed, missing and filled surfaces for primary teeth (dmfs) nor decayed, missing and filled surfaces for permanent teeth (DMFS) differed significantly between the probiotic and placebo groups (p > 0.05). MS and LBC levels were similar in both groups (p > 0.05). RAPD-PCR showed no evidence of oral colonisation with LF19 in the study group. It is concluded that an early intervention with LF19 did not affect the frequency of dental caries, MS or LBC. LF19 did not establish itself as a permanent facet of the oral microbiota in any of the subjects included in this study.