Our aim was to compare plaque fluoride and the level of mutans streptococci in saliva and plaque before and 1 and 2 years after discontinuation of water fluoridation in Kuopio, Finland. For comparison, a low-fluoride community was included in the study. Pooled plaque and saliva were collected from a random sample of 12-year-olds in both communities (n = 139). Enumeration of mutans streptococci in plaque was made on MSB agar and the level of salivary mutans streptococci was measured using the Strip mutans method. Fluoride was analyzed using a fluoride specific electrode. Caries, gingival status, fluoride varnish applications and self-reported oral health habits were recorded at baseline. Before discontinuation of fluoridation, the level of mutans streptococci in saliva was significantly lower in the fluoridated than in the non-fluoridated community. The difference in plaque mutans streptococci was not statistically significant. After discontinuation of water fluoridation, there was a significant shift towards elevated values of salivary mutans streptococci in the fluoridated community, but the level of mutans streptococci in plaque remained at the baseline level. There was no significant difference between the communities in the fluoride content of plaque either before or after discontinuation of fluoridation. From the background factors, only caries scores (higher in the non-fluoridated community) and oral hygiene (better in the non-fluoridated community) were significantly different between the communities.