The calcineurin inhibitors, cyclosporine and tacrolimus, are pivotal immunosuppressants in renal transplantation, but produce a cascade of acute (functional) and chronic (fibrotic) injurious events that contribute to chronic allograft nephropathy (CAN). Using the rat salt depletion model of calcineurin inhibitor toxicity, this study aimed to examine the effects of clinically relevant combinations of cyclosporine, tacrolimus and sirolimus on renal functional, structural and molecular markers of injury. Further, the effect of pirfenidone when added to these drug combinations was examined. There were differences in the effects of cyclosporine and tacrolimus on functional and molecular variables, with tacrolimus displaying more favourable results. As sole therapy, sirolimus had no effect on renal function or messenger RNA expression. Deterioration in renal function and a deleterious effect on molecular markers of fibrosis were seen when cyclosporine and sirolimus were combined at high doses; at lower doses, favourable outcomes for these end-points were elicited. When sirolimus and tacrolimus were combined, renal function worsened and the beneficial molecular effects of tacrolimus were reversed. Pirfenidone's actions were non-dose dependent and beneficial effects for renal function and molecular markers were demonstrated. The effect of pirfenidone on renal function has not previously been described. There were no differences in urinary protein or interstitial fibrosis measurements across the groups. Without fibrosis, it is impossible to say whether pirfenidone acted in a truly antifibrotic manner. However, the molecular changes possibly represent interim markers of fibrosis, suggesting such an effect may have been developing.