Carbon monoxide (CO) was measured in kitchens using wood or natural gas (NG) as cooking fuels in a semi-rural community, 50 kilometers from Karachi, Pakistan. A stratified random sub-sample based on fuel type and median income was taken from an established cohort who delivered a singleton live birth during 2000-02. Eight-hour daytime concentrations were obtained in 51 wood users and 44 NG users from December 2005 to April 2006. None of the cooking areas had chimneys; 86% of wood and 80% of NG users cooked in separate kitchens. Geometric mean (GM) CO concentration in wood users was 19.7 ppm (geometric standard deviation (GSD) 12.1) compared to 5.4 ppm (GSD 2.4) in NG users (p<0.001). Fuel burning duration and time spent in kitchen by participants were correlated (r= 0.72, p<0.01). The US Environmental Protection Agency standard of 9 ppm for eight hours for CO was exceeded in 88% of wood users compared to 27% of NG users. Cooking with wood fuel exposed the women to hazardous concentrations of CO that were significantly higher than using NG fuel.