Tuberculosis being an airborne infectious disease causes up to 2 million deaths yearly in the world. Rifampicin (RIF) is one of four first line antibiotics used to treat TB. It’s the 4th leading cause of deaths in Kenya at 6.3% of all causes of deaths, according to the National Strategic plan for Tuberculosis, leprosy and Lung Health (2015). Kenya is ranked 15 th of 22 high burdened TB countries all accounting for more than 80% of the world’s TB cases hence the need for research for mitigation and eradication purposes. This research was carried out to scrutinize impact of the new diagnostic use of GeneXpert assay to analyze TB burden, and Rifampicin resistant Mycobacterium tuberculosis considering age, gender, type of patient and facility. A laboratory investigation was done using a molecular based test called gene expert system to simultaneously detect M. tuberculosis and Rifampin resistance. Data analysis was done using SPSS 20; to determine frequencies and crosstabs. Of the 90 samples analyzed it was found that there is a 17.8% rate of Mycobacterium tuberculosis and 5.6% are Rifampicin resistant. The most affected people were aged 61-65 at 4.4%, case detection with GeneXpert is more accurate than microscopy .