The counts of cariogenic bacteria lactobacilli and mutans streptococci have been studied and correlated with sugar intake. This study was to investigate the association between salivary lactobacilli and mutans streptococci counts with sweet food eating behavior and sweet sensitivity among 120 Malaysian women (101 ethnic Chinese, 19 ethnic Indians), while taking into account anthropometric and menstruation variables. Demographics, anthropometric measurements and menstrual history were taken. Hedonic preference, intake frequency of a list of sweet foods, intensity perception and pleasantness ratings of sweet stimuli were assessed. Saliva was collected for lactobacilli and mutans streptococci culture. We found that centrally obese subjects (high waist circumference and waist-hip ratio) had significantly higher salivary lactobacilli and mutans streptococci counts (all p<0.05), while overweight and high total body fat subjects had significantly higher salivary mutans streptococci counts (p<0.001). The sweetness intensity perception of chocolate malt drinks was significantly lower in women who were in their pre-menstrual (post-ovulation) phase. However, menstruation variables (menstrual phases, regularity and pre-menstrual syndromes) did not play a role in determining compulsive eating, sweets/chocolate craving and salivary lactobacilli and mutans streptococci counts. Taken together, salivary lactobacilli and mutans streptococci counts of the Malaysian women are associated with central obesity, but not sweet food eating behaviour, sweet sensitivity and menstruation variables. Salivary microbiome analysis could be useful as a potential diagnostic indicator of diseases such as obesity.