We investigated the effects of ileum allotransplantation and chronic graft rejection on the synthesis and absorption of cholesterol. Twenty pigs underwent intestinal transection or ileum transplantation, in which the distal half of the jejunoileum was replaced with an ileal autograft or allograft. Conventional triple therapy with cyclosporine (10 mg/kg per day), azathioprine and methylprednisolone was tapered to cyclosporine (5 mg/kg per day) after 10 weeks. Serum lathosterol and campesterol, respective markers of cholesterol synthesis and absorption, were determined and related to graft histology. When compared to transected controls, auto- and allotransplantation of ileum similarly increased ( P<0.05) lathosterol and decreased ( P<0.01) campesterol for 12 weeks, despite normal graft histology. Chronic graft rejection progressed between 12 and 18 weeks, when a further increase in lathosterol (+104%) and decrease in campesterol (-67%) was observed. Obliteration of mesenterial arteries in chronically rejecting grafts was associated with high cholesterol synthesis ( R=0.975, P=0.0512). Auto- and allotransplantation of the ileum similarly modulate synthesis and absorption of cholesterol in pigs with non-rejecting grafts. Chronic rejection of the ileal graft appears to markedly increase cholesterol synthesis, which may primarily result from impaired ileal reabsorption of bile acids due to gradual obliteration of mesenterial arteries (chronic rejection). Serial measurements of cholesterol synthesis and bile acid absorption may prove to be a useful tool in the diagnosis of chronic rejection-associated small intestinal graft dysfunction.