Analysis of whole-genome data from people with multiple system atrophy (MSA) has identified novel genetic loci associated with the disease. The study, which included data from 888 people with MSA and 7,128 healthy control individuals, revealed four risk loci, and functional analysis indicated the involvement of three genes at these loci — USP38-DT, KCTD7 and lnc-KCTD7-2. The work provides insight into the currently unknown genetic architecture of MSA, and the publicly available data that were generated will facilitate further investigation.