Objective To investigate the clinical application value of genechip detection system in the mycobacterial species iden-tification and drug resistance analysis .Methods The specimens of sputum ,punctured pus ,pleural and abdominal ascites ,cerebro-spinal fluid and so on were performed the Mycobacterium DNA detection by using the gene chip technique .Then Mycobacterium tuberculosis positive samples were further performed the drug-resistant analysis .Meanwhile the Ziehl-Neelsen acid-fast staining was adopted to detect the sample .The positive rates were compared between the two groups .And TB-IGRA was used to examine the tubercle bacillus infection in partial patients .Results In 4402 samples ,137 cases (3 .36% ) of M ycobacterium tuberculosis (MTB) and 11 cases(7 .4% ) of non-tuberculosis mycobacterium(NTM) were detected .Puncture solution ,bronchoalveolar lavage fluid and tissue specimen had higher positive rate .In the 137 positive M TB samples by rifampicin-resistant gene rpoB ,isoniazide-re-sistant gene katG and inhA detection ,22 cases of resistance gene mutations were detected ;the positive rate of genechip for detecting sputum ,cerebrospinal fluid ,hydrothorax and ascites was higher than that of acid-fast staining .TB-IGRA detection had higher pos-itive rate of TB infection than genechip .Conclusion The genechip detection system can directly conduct Mycobacterium identifica-tion and drug resistance analysis ,which is especially suitable for sputum ,cerebrospinal fluid ,hydrothorax and ascites samples ,and which is simple and rapid with higher sensitivity and good specificity .