To compare the antimicrobial efficiency of chlorhexidine and cacao bean husk extract mouthrinses in children. A randomised comparative study which employed purpose sampling. Study was conducted on 50 children of both sexes aged 6-10 years old. A group of 25 children were given 10 ml of 0.2% chlorhexidine mouthrinse and another 25 children were given 10 ml of 0.1% cacao bean extract mouthrinse to rinse twice daily for about 30 seconds. The salivary samples were collected from each child in Dentocult SM vials on day one (pre-rinse) and after 7 days, 1 month and 2 months. The readings were tabulated and subjected to statistical analysis. Mann-Whitney test and the p-value were used for statistical analysis. There was significant reduction in streptococcus mutans counts in saliva at all follow-up intervals for both mouthrinse groups. However, there was no significant difference in reduction of streptococcus mutans counts in saliva, between chlorhexidine mouthrinse group and cacao bean husk extract mouthrinse group. Cacao bean husk extract mouthrinse can be used in children as an alternative to chlorhexidine mouthrinse as it has similar antimicrobial properties and evades the side-effects of the latter.