Our results present the most detailed comparison to date of the genetic risk underlying BP and SCZ. We identify six genome-wide significant loci associated with a combined BP+SCZ phenotype compared to controls, including a novel locus near PIK3C2A. At the same time, we demonstrate the ability to create a polygenic risk score from a GWAS of BP vs SCZ that significantly discriminates between the two disorders at the level of molecular genetic variants. Additionally, we found a strong correlation between BP polygenic score and the manic symptom dimension in SCZ cases.