Molecular assays performed for diagnostic and genotyping purposes can provide data that are relevant to a number of clinical and public health situations. This review describes molecular methods currently used to identify, characterize, and genotype (or DNA fingerprint) members of the Mycobacterium tuberculosis complex. In addition, strategies for improving current methods are outlined; recommendations for integrating genotyping data into public health programs are presented; and the necessity for reducing turnaround times for reporting genotyping data, through development of 'real time' universal genotyping programs, is stressed.