Abstract: Objective To investigate toxicological indicators of drinking water from self-drilled wells in rural area of Haidian district of Beijing and to provide a basis for improving drinking water quality. Methods A total of 911 drinking water samples from self-drilled wells in rural area of Haidian district were collected using stratified random sampling from 2011 to 2014 and toxicological indicators of the water samples were evaluated according to “Hygiene Standard for Drinking Water”(GB5749-2006).The effects of well depth, pollution sources, and disinfection facilities on the toxicological indicators were analyzed. Results During the period, the overall qualification rate of toxicological indicators for the samples detected was 94.51%;of the.911 water samples, 19(2.09%)and 27(2.96%)were unqualified for fluoride and nitrate nitrogen.Compared to the water samples from the self-drilled wells of more than 60 meters in depth, without pollution source at a distance of less than 50 meters around, and with normal operation of disinfection facilities, significantly lower overall qualification rate of toxicological indicators was observed for the samples from the wells less than 60 meters in depth (91.10% vs.97.19%, χ²=15.416), with pollution sources at a distance of less than 50 meters around (88.51% vs 97.29%, χ²=25.852), and with abnormal operation of disinfection facilities (83.94% vs.97.67%, χ²=52.290)(P < 0.001 for all). Conclusion Fluoride and nitrate nitrogen are major unqualified toxicological indicators and the depth of well, pollution source around the well, and operation status of disinfection facility are major influencing factors of overall qualification rate of toxicological indicators for the drinking water from self-drilled wells in rural area of Haidian district of Beijing.