A deficiency in phosphorylase kinase is responsible for several forms of glycogen storage disease which differ in heredity and affected tissues. This is so because phosphorylase kinase consists of four different subunits and has multiple tissue-specific isoforms. To elucidate the molecular basis of phosphorylase kinase deficiencies, the cDNAs encoding the subunits alpha and beta were cloned and sequenced. Each subunit was shown to be encoded by a single gene. The alpha subunit gene was mapped to chromosome Xq12-q13 and the beta subunit gene to chromosome 16q12-q13. Isoform cDNAs reveal differential mRNA splicing. Thus, the stage is set for the molecular characterization of the genes and their deficiency mutations.