The brainstem houses numerous nuclei and tracts that serve vital functions. Genome-wide associations with brainstem substructure volumes have been explored in European individuals, yet other ancestries remain under-represented. Here, we conduct cross-ancestry genome-wide association meta-analyses in 103,098 individuals for brainstem and 78,062 individuals for eight substructure volumes, including 7094 Chinese Han individuals. We identify 713 locus-trait associations with brainstem and substructure volumes at P < 5.56 ×10-9, comprising 569 new associations. Two associations show different effect sizes, while 496 associations have similar effect sizes between ancestries. We prioritize 186 genes associated with brainstem volumetric traits. We find both shared and distinct genetic loci, genes, and pathways for midbrain, pons, and medulla volumes, along with the shared genetic architectures related to disease phenotypes and physiological functions. The results provide new insights into the genetic architectures of brainstem and substructure volumes and their genetic associations with brainstem physiologies and pathologies.
© 2025. The Author(s).