The molecular signaling pathway linked to muscle regeneration has not yet been identified. Previously, we demonstrated that mice treated with cyclosporin A (CsA), a calcineurin inhibitor, failed to regenerate normally after muscle damage. Using reverse transcription (RT)-PCR, Western blot and immunohistochemical analysis, we investigated whether the amounts of nuclear factor of activated T cells (NFAT), myocyte-enhancer factor 2 (MEF2), the MyoD family, Id-1, and Smad3 change in the regenerating muscle after CsA treatment. Adult male ICR mice were subjected to a bupivacaine injection into the tibialis anterior muscle, and were treated with either CsA (25 mg/kg) or vehicle once daily. They were killed at 1, 2, 4, 6, 9 and 14 days post injury. RT-PCR analysis did not show a significant difference in MEF2s, MyoD and myogenin mRNA levels in the regenerating muscle in either placebo- and CsA-administered mice. In contrast, a significant increase in MRF4 mRNA was seen in CsA-administered mice compared to the placebo-treated mice at 4 and 9 days post surgery. In CsA-treated mice, the level of Id1 mRNA was elevated at day 9 relative to the placebo-treated mice. After 6 days, the CsA-treated mice possessed more abundant proliferating cell nuclear antigen (PCNA) and cyclin D1 protein in many satellite cells and/or myoblast-like cells in the regenerating muscle. The amount of myostatin, TGF-beta2 and Smad3 mRNA and proteins was increased more markedly in the mice treated with CsA. After 9 days, many satellite cells and/or myoblasts showed apparent co-localization of both MyoD and Smad3 in CsA-, but not in placebo-, treated mice. Our results demonstrated that CsA treatment upregulates Id1 and Smad3 expression and delays skeletal muscle regeneration in vivo.