Cyclosporine A (CsA), a calcineurin inhibitor produced by the fungi Trichoderma polysporum and Cylindrocarpon lucidum, is an immunosuppressant prescribed in organ transplants to prevent rejection. Its adverse effect on renal dysfunction has limited its use in a clinical setting. Apigenin (4',5',7'-Trihydroxyflavone), a herbal extract, with anti-inflammatory and anti-tumour properties, has been investigated for properties to reverse this adverse effect. This research was conducted to establish a standard protocol for immunohistochemical estimation of Transforming Growth Factor beta (TGF-beta) expression, as an indicator of Cyclosporine A induced damage, and to observe whether apoptotic index and TGF-beta expression can be used to assess effects of Apigenin on CsA induced renal dysfunction. Six groups of 5 male Sprague-Dawley albino rats each were dosed once daily for 21 days, as follows: (1) negative control--oral corn oil, (2) positive control--Cyclosporine A (25 mg/kg), (3) Group 3--Apigenin (20 mg/kg), (4) Group 4--Cyclosporine A (25 mg/kg) +Apigenin (10 mg/kg), (5) Group 5--Cyclosporine A (25 mg/kg) +Apigenin (15 mg/kg) and (6) Group 6--Cyclosporine A (25 mg/kg) +Apigenin (20 mg/kg). Cyclosporine A was administered intra-peritoneally while Apigenin was given orally. The rat kidneys were harvested and examined microscopically to assess the apoptotic index, and stained by immunohistochemistry for multifunctioning polypeptide TGF-beta expression. A high apoptotic index and TGF-beta intensity was observed in the Cyclosporine A group. Apigenin significantly reduced the both apoptotic index and TGF-beta intensity. The apoptotic index correlated with TGF-beta intensity, especially in glomeruli. This study indicates that Cyclosporine A can enhance the TGF-beta expression in rat kidney, signifying accelerated apoptosis. TGF-beta and apoptotic index may be used to assess Apigenin and its effect on Cyclosporine A induced renal damage.