Background: The HAIN GenoType®MTBDRplus (first line) and GenoType MTBDRsl (second line) line probe assays are nucleic acid amplification tests that work with PCR technology. The GenoType MTBDRsl line probe assay (LPA) is recommended by WHO as a replacement test instead of culture based drug susceptibility testing of fluroquinones & second line injectables regardless of smear status. However, the laboratory staff noticed poor performance of this assay when done directly from smear negative sputum samples. Objective: This audit aimed to determine the percentage of successful line probe assays in patients with smear negative and smear positive MTB. Method: The investigators determined the number of LPAs performed over a three-month period. They then determined the number of successful LPAs (first line and second line) and correlated them with smear status. Results: A total of 319 LPAs were performed. One hundred and eighty-four were first line LPAs and 135 were second line LPAs. All of the first line LPAs yielded successful results; 104/184 (56.52 %) were smear positive whereas 80/184 (43.48%) were smear negative. Seventy-three out of the 135 second line LPAs were successful and smear positive. The remaining 62 were smear negative, of these 27 (27/62; 43.55%) were successful the remaining 35/62 (56.45%) were unsuccessful and needed repeat LPAs from the cultured isolate. Conclusion: Due to rising reagent costs it is recommended that laboratories check the percentage of successful second line LPAs and investigate other methods to determine second line resistance in smear negative samples such as the Xpert® MTB/XDR.