Abstract Background/Purpose Medial layer hypertrophy of hepatic arterial branches may be associated with biliary atresia (BA) pathogenesis. This study aimed at evaluating medial layer thickness in hepatic arterial branches at portoenterostomy and liver transplantation. Methods The authors evaluated 1274 arterial branches both in BA cases and in control subjects involving a total of 1108 arterioles and 166 arteries. Arterial branch characteristics were morphometrically evaluated in 47 BA patients at the time of portoenterostomy. Controls were patients with intrahepatic cholestasis (n = 3), immature neonates (n = 7), and infants (n = 7) without liver disease. Progression of medial layer thickening between the time of portoenterostomy and transplantation was evaluated in 7 BA patients. Biliary atresia patients at the time of transplantation were compared with non–BA-transplanted patients (n = 4). Results The arterial medial layer of BA cases at portoenterostomy was thicker than that of infants without liver disease ( P = .03). The arterial medial thickness increased during the interval between portoenterostomy and transplantation ( P = .05). Arterioles and arteries with thickened medial layers were found in transplanted BA patients but not in patients transplanted for other liver diseases ( P = .05 and P = .01). Thickening of the medial layer of the hepatic arteries was associated with focal distribution of interlobular bile ducts in portal spaces in BA ( P = .02). Conclusions In BA, there is a progressive thickening of the arterial medial layer, suggestive of vascular remodeling, which is associated to the disappearance of interlobular bile ducts.