Rheumatic heart disease (RHD), an autoinflammatory heart disease, was recently declared a global health priority by the World Health organization. Here we report a genome-wide association study (GWAS) of RHD susceptibility in 1,163 South Asians (672 cases; 491 controls) recruited in India and Fiji. We analysed directly obtained and imputed genotypes, and followed-up associated loci in 1,459 Europeans (150 cases; 1,309 controls) from the UK Biobank study. We identify a novel susceptibility signal in the class iii region of the human leukocyte antigen (HLA) complex in the South Asian dataset that clearly replicates in the Europeans (rs201026476; combined odds ratio 1.81, 95% confidence intervals 1.51-2.18, P = 3.48×10 −10). importantly, this signal remains despite conditioning on the lead class i and class ii variants (P = 0.00033). These findings suggest the class III region is a key determinant of RHD susceptibility offering important new insight into pathogenesis while partly explaining the inconsistency of earlier reports. Rheumatic heart disease (RHD) is one of the leading causes of cardiovascular death and disability in children and young adults globally 1,2. The disease is caused by an aberrant immunological response to Streptococcus pyogenes (also termed group A streptococcus), a process that causes scarring and thickening of the heart valves 3. Beginning in childhood, RHD gradually causes the heart to fail, leading to complications including arrhythmias, stroke and early death 3. A recent analysis by the Global Burden of Disease Consortium estimated 319,400 deaths and 10.5 million disability-adjusted life-years (DALYs) each year globally due to RHD 2 , a substantial disease burden, especially in comparison to other diseases with infectious aetiology 4,5. In 2015, the highest age-standardised mortality due to RHD outside Oceania was observed in South Asia, with a total of 119,110 deaths in India alone 2. While much about the pathogenesis of RHD remains uncertain, the disease is generally considered to be autoimmune in nature with several factors relating to the pathogen itself and the environment of the host likely to impact risk 6. In addition, host genetic variation is widely thought to play a role 7 , not least because of the higher concordance of acute rheumatic fever among monozygotic compared to dizygotic twins 8. To date, two genome-wide association studies (GWAS) have been published: the first set in diverse populations in Oceania 9 , and the second in Aboriginal Australians 10. Consistent with several studies predating the GWAS era, which linked the disease to the human leukocyte antigen (HLA) complex on chromosome 6 11 , the Australian study found a signal that peaked in the class II region of HLA just below genome-wide significance, which was fine-mapped to a single nucleotide polymorphism (SNP) located within intron 1 of HLA-DQA1 10. The pre-GWAS results should be