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Caspase-3 plays a key role in apoptosis, but the involvement of apoptosis and caspase-3 in mediating long-term ischemia/reperfusion (I/R) and immunosuppressive injury are not fully defined. The present study was undertaken to investigate apoptosis and caspase-3 in a renal I/R injury rat model with or without immunosuppression.The right renal pedicle was clamped for 45 minutes and left nephrectomy was induced. Cyclosporin A (CsA), tacrolimus (Tac), rapamycin (Rap), or mycophenolate mofetil (MMF) were administered daily. Animals were killed at 16 weeks, and the levels of apoptosis (with in situ end-labeling fragmented DNA), caspase-3 protein (with immunohistochemistry, Western blotting, and activity assay), and messenger RNA (mRNA; with quantitative reverse-transcriptase polymerase chain reaction) were evaluated.Kidneys with I/R injury showed increased apoptosis in tubular and interstitial areas compared with control kidneys. Tacrolimus, Rap, and MMF significantly reduced apoptosis, but CsA did not. Distribution of full-length caspase-3 widened in I/R–injured kidneys from normal distal tubules and collecting ducts to dilated proximal tubules and expanded interstitium, whereas active caspase-3 was mainly scattered in damaged tubules and interstitium. Active caspase-3 staining and 24-kDa active caspase-3 protein was enhanced in I/R–injured and CsA-treated kidneys, but decreased by Tac, Rap, and MMF. These results were also consistent with changes in caspase-3 activity. Although caspase-3 mRNA levels were significantly increased in uninephrectomy and I/R–injured kidneys, they were not significantly affected by the immunosuppressants. In addition, all changes detected were positively correlated with renal structure and function.Apoptosis and caspase-3 are not only involved in the long-term renal I/R injury, but also mediate the divergent effects of immunosuppression in this model.