Miswak, a chewing stick prepared from the roots, twigs or stems of Salvadora persica. The beneficial effects of miswak in respect of oral hygiene and dental health are partly due to its mechanical action and partly due to its pharmacological actions. The aim of this study was to evaluate the effects of miswak sticks, miswak extract and toothbrush/toothpaste as antimicrobial agents on total bacterial count in the saliva, and to study the effect of miswak stick, toothbrush/toothpaste and saline on salivary Streptococcus mutans (S. mutans) and lactobacilli in vivo. The study clarified that there was a marked reduction in the total bacterial count among all groups. The reduction was 100%, 100%, 97.5% and 67.5% among users of miswak stick, miswak extract, toothbrush/toothpaste and saline (control), respectively. The results of the current study also showed marked reduction of S. mutans in 66.7% of the individuals using miswak and among individuals using toothbrush/toothpaste, whereas the reduction was only 29.2% among saline users. The reduction of lactobacilli was 62.5%, 58.3% and 54.2% by using miswak stick, toothbrush/toothpaste and saline, respectively. The difference was not statistically significant. It can be concluded that miswak has an antimicrobial effect comparable to the use of fluorinated toothpaste. It was clear from the current study that the Caries Risk Test (CRT) kit is a rapid and a simple, semi-quantitative method for counting lactobacilli and S.mutans, which can be used in dental clinics without the need for trained technicians. It is recommended that further studies can be performed on larger sample size of patients, at high risk of developing dental caries.