The most commonly used conventional Lowenstein Jensen (L.J) culture method requires at least 6 to 10 weeks of incubation due to the slow growth rate of the Mycobacterium tuberculosis complex. Today, there are liquid automated systems to detect mycobacteria than faster conventional LJ culture method. In this study, we aimed to compare of the VersaTrek system and BACTEC MGIT 960 system for the contamination rate and recovery of mycobacteria from clinical specimens. The recovery rates of mycobacteria were detected as 4% (2/50) for both of the VersaTrek and MGIT 960 systems. No statistically significant difference was detected for the recovery rates of mycobacteria in both of the systems (p>0.05). Two strains were detected on 12 and 15 day in MGIT 960 system. Two strains were detected on 15 and 20 day in VersaTrek system. No statistically significant difference was detected for the time of detection of mycobacteria in both of the systems (p>0.05). The contamination rates were found as 10% (5/50) and 6% (3/50) in MGIT 960 and VersaTrek, systems respectively (p>0.05). No statistically significant difference was detected for the contamination rates for both of the systems. Antituberculosis resistance tests were performed using with antituberculosis agents in MGIT 960 and VersaTrek systems. The two strains were found sensitive against to streptomycin, isoniazid, rifampicin and ethambutol in MGIT 960 system. The two strains were found sensitive against to isoniazid, rifampicin and ethambutol in VersaTrek system. Streptomycin was not used in VersaTrek system because there is no standardization for streptomycin. We also examined the time of detection of 5 confirmed M. tuberculosis complex members in MGIT 960 and VersaTrek systems. When the time of detection in MGIT 960 and VersaTrek systems were compared, no statistically significant difference was found (p>0.05). In conclusion, no substantial difference has been observed between MGIT 960 and VersaTrek systems for M. tuberculosis isolation and contamination rate. We believe that VersaTrek media, which is going to be put into use in Turkey, is easy for application and follow up, gives rapid and sensitive results and that it can be used in routine alike MGIT media.