Objectives In order to understand the sanitary situation of the rural drinking water safety project in Yunnan province, and to provide scientific basis for preventing water-borne infection and controlling drinking water relevant public health events.

Methods The basic situation of water supplies in the rural drinking water safety project and water samples were collected and investigated according to the National Sanitary Surveillance Scheme for Rural Drinking Water Project proposed by the National Public Health Campaign Committee.Water samples were examined according to the Standard Examination methods for Drinking Water.

Results In 1 067 water supplies of the project, 47.24% of them had no enough treatment facilities, only 14.34% of them had completed treatment facilities. Surface water was the main type of water source, which accounted for 62.79%. The 18 indexes detected in 4 268 water samples, only those in 1 253 (29.36%) water samples reached the standard quality for drinking water in China. The qualified rate of treated water was 30.04% and the qualified rate of tap water was 28.68%(P>0.05). The qualified rate in dry period was 36.22%, and was 22.02% in wet period(P < 0.05). The qualified rate of 18 examined indexes which was lower than 90% were total coli forms, visible substance, total bacteria counts and turbidity.

Conclusions Water treatment facilities in most of water supplies in the rural water drinking safety project in Yunnan were insufficient, and the administration was not perfect. The qualified rate of drinking water was lower in microbial index and general sensory indexes, and there were hidden dangers in drinking water safety.