Tuberculosis is an important reason of mortality and morbidity all over the world and is particularly relevant in developing countries like India where the disease is endemic. Female reproductive system is very susceptible to this infection but the clinical presentation of this disease in female reproductive tract is protean in nature and the disease could remain completely asymptomatic so a study was carried out for comparative evaluation of standard and molecular techniques to detect Mycobacterial infections among infertile females and to evaluate the efficacy of molecular technique (RT-PCR) in comparison to other standard (Liquid Culture and AFB Staining) techniques along with the determination of drug susceptibility pattern of confirmed MTB cases using first & second line of drugs and speciation of the isolated Non-tuberculous Mycobacterial (NTM) strains using genotypic mycobacterium assay. According to the literature, NTM's are found to be increasingly important pathogens causing male genital infections and infertility, but this study gave an insight that NTM's can even lead to female infertility and infections.