Background: Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a pulmonary disease caused by Mycobacterium tuberculosis. However antibiotic resistance to RIF is prevalent despite an apparent fitness cost. RIF resistance is primarily caused by mutations in the RIF resistance determining region in the rpoB gene, at the cost of slower growth in rich media. Compensatory mutations in the genes rpoA and rpoC have been shown to alleviate this fitness cost. These compensatory mutations may explain how RIF resistant strains have spread so rapidly. However, the effect of compensation on transmission is still unclear, partly because of uncertainty over which rpoABC mutations compensate for which RIF resistance markers. Objectives: We performed an association study on a globally representative set of 4309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations. Results and Conclusions: Only 20.0% (216/1079) of RIF resistant isolates carried previously reported high-probability compensatory mutations, suggesting existence of other compensatory mutations. Using a strict phylogenetic approach, we identified 18 novel putative compensatory mutations in rpoC, rpoB, and rpoA. Novel and previously reported compensatory mutations were strongly associated with the RIFR marker rpoB:S450L, suggesting compensation may be specific to particular RIFR markers. These findings will aid identification of RIF-resistant M. tuberculosis strains with restored fitness. Such strains pose a greater risk of causing resistant outbreaks.