© 2019, Nihon University, School of Dentistry. All rights reserved. Coffee is a widely consumed beverage containing organic compounds with antibacterial activity. To investigate its possible effect on the growth of oral indigenous microbiota, saliva samples collected from nine young adults were inoculated into brain heart infusion (BHI) medium with or without addition of coffee compounds and cultured at 37°C in 5% CO2 for 12 h. The total bacterial density and composition after cultivation for 0, 6, and 12 h were determined by quantitative PCR analysis and 16S rRNA gene sequencing, respectively. The increase in total bacterial load was significantly inhibited by addition of the coffee compounds. The microbiota was mostly composed of Streptococcus species after culture in BHI medium regardless of the addition of coffee compounds. The proportion of Streptococcus salivarius was significantly reduced after addition of coffee relative to that in untreated medium alone, whereas the proportions of Streptococcus mitis and Streptococcus infantis were increased. These results suggest that exposure to coffee affects the composition of the oral Streptococcus population, in addition to inhibiting the overall growth of salivary bacteria. Considered in the light of data from earlier epidemiological studies, it is possible to conclude that coffee consumption contributes to better health.