Our exploratory study found novel splicing associations with AUD. We found support for our three hypotheses, such that: (1) polygenic scores were increased in those with AUD, (2) specific SNPs were associated with abnormal mRNA splicing events in multiple brain regions and (3) DNA variants in and around differentially spliced genes contributed to the heritability of AUD. Altogether, we used a handful of methods that provided evidence implicating genetic factors in AUD-related alternative mRNA splicing. These data add another layer to the neuroepigenetic understanding of compulsive alcohol use.