Abstract: Objective To understand the diagnostic accuracy of reported typhoid cases through surveillance system in five areas of south Xinjiang, and the performance of diagnosis and treatment of typhoid fever and paratyphoid fever in grass root medical institutions. Methods The clinical diagnosed and confirmed typhoid and paratyphoid cases reported in the five areas during January 1-August 31, 2016 were evaluated according to the national typhoid and paratyphoid diagnosis criteria to verify the diagnosis accuracy. The performance of laboratory detection of typhoid and paratyphoid was surveyed in some hospitals. A questionnaire survey was conducted in clinical doctors to learn about their knowledge about typhoid and paratyphoid fever and information about related training. Results Of the 49 typhoid and paratyphoid fever cases reported in five areas of south Xinjiang during this period, the accuracy of clinical diagnosis was 6.67% (1/15), and the accuracy of case confirmation was 14.71% (5/34). A total of 32 medical institutions were investigated. Only 5.88% (1/17) of township hospitals were able to carry out bacterial culture, and 100% of them did not carry out Widal test. Of the 105 doctors surveyed, the correct answer rate for clinical case definition was only 7.62%, and the correct answer rate of case confirmation definition was only 11.43%. The doctors who had attended related training had higher correct answer rates compared with those who received no training. Conclusion This survey found that limited grass root medical institutions conducted bacterial culture and Widal test, and the doctors were not fully understood the diagnosis criteria of typhoid and paratyphoid fever. It is suggest to conduct free typhoid and paratyphoid verification and detection by county CDCs and strengthen the medical staff training in grass root medical institutions for the timely diagnosis of suspected cases and the sensitivity of outbreak detection.