Myosin heavy chain (MHC) mRNA isoforms were quantified in soleus (SOL) and gastrocnemius (GAS) muscles from rats exposed to 14 days of either hindlimb unweighting (HU), clenbuterol treatment (CB), or HU combined with CB treatment (HU-CB). All conditions induced in SOL a shift from slow to faster MHC mRNA isoforms and an upregulation of MHCI alpha. Increases were highest with CB, lowest with HU-CB, and coincided mainly with elevations in MHCIIa mRNA isoforms. The changes in MMC mRNA levels in GAS muscle corresponded to fast-to-faster transitions. Elevations in MHCI alpha mRNA were smaller than in SOL and seemed to occur in parallel with decreases in MHCI beta. Taken together, our results suggested that MHCI alpha is expressed in transforming rat slow and fast muscles, most likely as an intermediate step between MHCI beta and MHCIIa.