BACKGROUND: The association between ambient air pollution and heart rate variability (HRV) has been well-documented. Little is known about the association of HRV at night with indoor air pollution and coffee consumption. The aim of this study was to investigate the association of HRV indices with indoor air pollution, working time and coffee consumption. METHODS: We recruited 60 young healthy convenient store workers to monitor indoor PM2.5 (particulate matter with an aerodynamic diameter </= 2.5 microm) exposures, coffee consumption (yes vs. no) and HRV indices during daytime (0700-1500 hours) and nighttime (2300-0700 hours). We used linear mixed effects models to assess the associations of HRV indices with indoor PM2.5 exposures and coffee consumption. RESULTS: We observed the inverse association between indoor PM2.5 exposures and HRV indices, with a decrease in all HRV indices with increased indoor PM2.5 exposures. However, the decrease was most pronounced during nighttime, where a 1 interquartile range (IQR) increase in indoor PM2.5 at 4-hr time-weighted moving average was associated with a change of -4.78% 5-min standard deviation (SD) of normal-to-normal intervals for 5-min segment (SDNN) and -3.23% 5-min square root of the mean squared differences of successive intervals for 5-min segment (r-MSSD). Effects of indoor PM2.5 were lowest for participants with coffee consumption during daytime. CONCLUSIONS: Indoor PM2.5 exposures were associated with decreased 5-min SDNN and 5-min r-MSSD, especially during nighttime. The effect of indoor PM2.5 on HRV indices may be modified by coffee consumption in young healthy convenient store workers.