This study, conducted on 25‐month denervated rat hindlimb muscles, was directed toward elucidating the basis for the poor regeneration that is observed in long‐term denervated muscles. Despite a ∼97.6% loss in mean cross‐sectional area of muscle fibers, the muscles retained their fascicular arrangement, with the fascicles containing ∼1.5 times more fibers than age‐matched control muscles. At least three distinct types of muscle fibers were observed: degenerating, persisting (original), and newly formed (regenerated) fibers. A majority of newly formed fibers did not appear to undergo complete maturation, and morphologically they resembled myotubes. Sites of former motor end‐plates remained identifiable in persisting muscle fibers. Nuclear death was seen in all types of muscle fibers, especially in degenerating fibers. Nevertheless, the severely atrophic skeletal muscles continued to express developmentally and functionally important proteins, such as MyoD, myogenin, adult and embryonic subunits of the nicotinic acetylcholine receptor, and neural‐cell adhesion molecule. Despite the prolonged period of denervation, slow and fast types of myosin were found in surviving muscle fibers. The number of satellite cells was significantly reduced in long‐term denervated muscles, as compared with age‐matched control muscles. In 25‐month denervated muscle, satellite cells were only attached to persisting muscle fibers, but were never seen on newly formed fibers. Our data suggest that the absence of satellite cells in a population of immature newly formed muscle fibers that has arisen as a result of continuous reparative myogenesis may be a crucial, although not necessarily the only, factor underlying the poor regenerative ability of long‐term denervated muscle. Anat Rec 263:139–154, 2001. © 2001 Wiley‐Liss, Inc.