A monoclonal antibody was used to prepare immunoaffinity columns that efficiently bind monoamine oxidase B activity but not monoamine oxidase A activity from detergent extracts of human liver mitochondria. The only discrete polypeptide component that eluted from affinity columns with potassium thiocyanate migrated in sodium dodecyl sulfate-polyacrylamide gels with an apparent molecular weight of 59,000, as expected for human monoamine oxidase B. These results support the hypothesis that there is an intrinsic structural difference between monoamine oxidase A and B and demonstrate that immunoaffinity chromatography can physically resolve the two enzyme species in liver extracts.