In this study, we set out to determine if alcohol affects splicing in the superior frontal cortex, nucleus accumbens, basolateral amygdala, and central nucleus of the amygdala. We found that mis-splicing in these regions occurs on a much broader scale than changes in gene expression, with thousands of transcripts being mis-spliced. Mechanistically, mis-splicing appears to be mediated by an increased expression of splicing factor heat shock protein family A (Hsp70) member 6 (HSPA6) and/or aberrant expression of lncRNAs related to splicing.