High concentrations of household air pollution (HAP) due to biomass fuel usage with unvented, insufficient combustion devices are thought to be an important health risk factor in South Asia population. To better characterize the indoor concentrations of particulate matter (PM2.5) and carbon monoxide (CO), and to understand their impact on health in rural southern Nepal, this study analyzed daily monitoring data collected with DataRAM pDR-1000 and LASCAR CO data logger in 2980 households using traditional biomass cookstove indoor through the Nepal Cookstove Intervention Trial-Phase I between March 2010 and October 2011. Daily average PM2.5 and CO concentrations collected in area near stove were 1,376 (95% CI, 1,331-1,423) μg/m3 and 10.9 (10.5-11.3) parts per million (ppm) among households with traditional cookstoves. The 95th percentile, hours above 100μg/m3 for PM2.5 or 6ppm for CO, and hours above 1000μg/m3 for PM2.5 or 9ppm for CO were also reported. An algorithm was developed to differentiate stove-influenced (SI) periods from non-stove-influenced (non-SI) periods in monitoring data. Average stove-influenced concentrations were 3,469 (3,350-3,588) μg/m3 for PM2.5 and 21.8 (21.1-22.6) ppm for CO. Dry season significantly increased PM2.5 concentration in all metrics; wood was the cleanest fuel for PM2.5 and CO, while adding dung into the fuel increased concentrations of both pollutants. For studies in rural southern Nepal, CO concentration is not a viable surrogate for PM2.5 concentrations based on the low correlation between these measures. In sum, this study filled a gap in knowledge on HAP in rural Nepal using traditional cookstoves and revealed very high concentrations in these households.