Myosin folding and assembly in striated muscle is mediated by the general chaperones Hsc70 and Hsp90 and involves a myosin specific co-chaperone related to the C. elegans gene unc-45. Two unc45 genes are found in vertebrates, a general cell isoform, unc45a, and a striated muscle specific isoform, unc45b. We have investigated the role of both isoforms of mouse Unc45 in myosin folding using an in vitro synthesis and folding assay. A smooth muscle myosin motor domain fused to GFP (MD::GFP) was used as substrate and folding was measured by native gel electrophoresis and functional assays. In the absence of Unc45, the MD::GFP chimera folds poorly. Addition of either Unc45a or Unc45b dramatically enhances the folding in a reaction that is dependent on Hsp90 ATPase activity. Unc45a is more effective than Unc45b with a higher apparent affinity and greater extent of folding. The Unc45/Hsp90 chaperone complex acts late in the folding pathway and promotes motor domain maturation after release from the ribosome. Unc45a behaves kinetically as an activator of the folding reaction by stimulating the rate of the Hsp90 dependent folding by >20 fold with an apparent Kact of 33 nM. This analysis of vertebrate Unc45 isoforms clearly demonstrates a direct role for Unc45 in Hsp90 mediated myosin motor domain folding, and highlights major differences between the isoforms in substrate specificity and mechanism.