To evaluate the application value of GeneXpert MTB/RIF system in the diagnosis of pulmonary tuberculosis (TB) among the TB suspects who sought health care for the first time. A total of 361 TB suspects, who visited Jiaxing 1st Hospital to seek health care for the first time from Jan 2015 to Dec 2016, were consecutively enrolled in the study. The sputum specimens were collected from those patients and smear microscopy, liquid culture, GeneXpert MTB/RIF test and solid drug susceptibility testing (DST) by using proportion method were performed. Finally, 184 cases (50.97%) were confirmed to have pulmonary TB while 162 cases (44.88%) were diagnosed to be pulmonary infections and 15 cases (4.15%) were diagnosed to be pulmonary infections caused by atypical mycobacteria. Among 361 TB suspects, the positive rate of GeneXpert MTB/RIF was 32.41% (117/361), which was significantly higher than the smear-positive rate (22.71%, 82/361) (χ 2=8.49, P<0.05); but the difference of the positive rate between GeneXpert and liquid culture (26.32%, 95/361) was not statistically significant (χ 2=3.23, P=0.072); the smear-positive rate was lower than that of liquid culture (26.32%, 95/361), but the difference was not statistically significant (χ 2=1.26, P=0.261). Among 184 cases with pulmonary TB, the positive rate of GeneXpert MTB/RIF was 63.59% (117/184) which was significantly higher than the smear-positive rate (36.41% (67/184)) and the liquid culture positive rate (48.91% (90/184)) respectively (χ 2=27.17, P<0.01; χ 2=8.05, P<0.05). Among 117 smear-negative pulmonary TB patients, the positive rate of GeneXpert MTB/RIF was 42.74% (50/117), which was significantly higher than that of liquid culture (24.79%, 29/117) (χ 2=8.43, P=0.004). If the clinical diagnosis result was regarded as a standard, the sensitivity of GeneXpert in TB suspects, who sought health care for the first time, was 63.59% (117/184), its specificity was 100.00% (177/177) and its correct indices was 0.64; if the result of solid DST with proportion method was regarded as a standard, the sensitivity of GeneXpert in TB suspects, who sought health care for the first time, was 4/5, its specificity was 97.70% (85/87) and its correct indices was 0.97. GeneXpert MTB/RIF technique has demonstrated a high capacity on detection of tuberculosis and rifampicin resistant TB in TB suspects, especially in smear-negative pulmonary TB patients.