The aim of this study was to compare the effect of two different chlorhexidine regimens, varnish and gel, on mutans streptococci (MS) in the margins of restorations and in saliva. Eighteen subjects (mean age 44 years) with >250,000 MS/ml saliva and with many restored teeth were assigned to three groups, each comprising 6 individuals. They were treated with: (1) Cervitec varnish, containing 1% chlorhexidine and 1% thymol; (2) placebo varnish, or (3) Corsodyl gel, containing 1% chlorhexidine. The varnish was applied on two separate occasions to all tooth surfaces at an interval of 3-4 days. The gel was applied for 3 x 5 min in individual applicators on 2 consecutive days. Plaque samples from 8-9 margins of restorations per subject, mainly in the premolar and molar region, and stimulated saliva samples were collected at baseline and after 1, 4, 8 and 12 weeks. The general finding was that the Corsodyl gel gave the most pronounced reduction of MS followed by the Cervitec varnish. According to repeated measures ANOVA, no significant differences could be demonstrated either for MS in margins or in saliva among the three groups (p = 0.06 for margins and p = 0.07 for saliva). However, within the groups, the reduction of MS over time was statistically significant, both in margins and in saliva (p < 0.001 and p < 0.05, respectively). Student-Newman-Keuls test showed that MS in margins were significantly reduced at most sampling occasions in both chlorhexidine groups: the reduction was more pronounced in the Corsodyl gel group. The conclusion from this study is that the 1% chlorhexidine gel Corsodyl, administered 6 times during 2 days, is more effective in suppressing MS in the margins of restorations and in saliva than the 1% chlorhexidine varnish Cervitec, administered twice within 3-4 days.