Objective. The aim of this study was to evaluate the effect on mutans streptococci and lactobacilli in saliva of mouthrinsing with essential oils and an alcohol-free chlorhexidine. Materials and method. Twenty healthy volunteers (mean age 59 years) participated in the double-blind randomized cross-over study. Three mouthrinses were used in 16 days rinsing periods in addition to their regular mechanical oral hygiene: a solution with essential oils (EO; Listerine), a solution with alcohol-free chlorhexidine (CHX; Paroex) and water (negative control). The mouthrinse periods were separated by 3-month washout periods. At days 0 (baseline) and 17 (end) of each mouthrinse period, paraffin stimulated whole saliva was collected in order to analyse CFU/ml saliva of mutans streptococci and lactobacilli. Results. Only the CHX rinse showed a significant difference for CFU mutans streptococci between baseline and end (p = 0.004). The CFU mutans streptococci at the end of the rinse periods showed statistically significant differences between CHX vs EO (p = 0.039) and CHX vs water (p = 0.022). The difference in CFU lactobacilli between baseline and end was significant for CHX (p = 0.031), but not for the other rinses. No statistically significant differences for lactobacilli were found at the end of the rinse periods between the mouthrinses. Conclusion. A significant reduction in amount of cariogenic bacteria in saliva was observed after 16 days of alcohol-free chlorhexidine mouthrinse but not after the essential oils rinse. The high number of participant's not changing to a bacterial class with a reduced number of micro-organisms showed that both rinses had little clinical significance as a caries preventing treatment method, which can decrease the number of CFU cariogenic micro-organisms.