Tuberculosis (TB) control programmes aim to prevent transmission of Mycobacterium tuberculosis by identifying and treating active cases of TB and ensuring that contacts are identified and screened for active and latent infection. It is also essential to rapidly detect and investigate outbreaks to confirm epidemiological links between cases or transmission settings in order to direct public health action. Genotype fingerprinting techniques, based on examining repetitive sequences of DNA present in the bacterial genome, can be used to identify genetically similar TB strains, which are considered part of the same molecular cluster and may be related by transmission. Combined with epidemiological information, genotype data can be used as a tool to detect outbreaks and ongoing transmission. It can also provide insight into risk factors associated with transmission in different populations and countries. This chapter describes the different genotyping methods available and explores their use in the study of transmission dynamics, phylogenetic analysis, the effects of lineage and drug resistance on transmission, the differentiation of reinfection and relapse, the occurrence of missed infections and the role of genotyping in public health through the identification of laboratory contamination and the investigation of outbreaks. The chapter will review what we have learned about transmission from using these methods and how this knowledge can be translated into public health practice and TB control.