This study attempted to compare Persian shallot aqueous extract with commercially available chlorhexidine mouth rinse with respect to their anti-microbial activity on salivary bacterial counts. Three groups of 10 volunteers with a healthy oral status, were randomly enrolled. Using sterile water as negative control, using 0.2% chlorhexidine as standard control and Persian shallot aqueous extract for test group. A single mouth rinse lasting 15 s of each mouth rinse was employed. Salivary bacterial counts were obtained by collecting unstimulated saliva samples at the beginning before rinsing for measurement of baseline count and 1, 5 and 24 h after rinsing with the assigned solution. Analysis of variance and Bonferroni post hoc tests were used to evaluate significant differences among groups. No significant differences among the allocated groups were detected at baseline. Chlorhexidine produced more significant reduction of salivary bacterial count relative to both shallot and distilled water control at 1 h. In addition, a significant difference at 1 h was also detected between both chlorhexidine and shallot extract with distilled water. Furthermore, at 5 h there was a significant difference in bacterial count between chlorhexidine and shallot extract. After 24 h, the level of bacterial count in shallot extract was still significantly lower than both chlorhexidine and distilled water control groups. The results of this study suggest that Persian shallot extract has more persistent inhibitory action than chlorhexidine mouth rinse lasting up to 24 h. Key words: Antimicrobial mouth rinse, Persian shallot extract, oral bacteria.