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Seven patients with diagnosis of biliary atresia (BA) and two patients with neonatal hepatitis were studied by electron microscopy. In all patients the diagnosis was done by clinical examinations, laboratory assays, histological studies by punch or surgical biopsies and or surgical examinations combined with intraoperatory cholangiography. The ultrastructural alterations found in both groups of patients were essentially similar to those described in other forms of cholestasis. In patients suffering from biliary atresia the main features found at hepatocytic livel were: Finely granular deposits of electron dense substance sometimes conforming lamellar structures; 2) Some increase and vesiculation of smooth endoplasmic reticulum membranes; 3) Reductions in number and length of sinusoidal microvilli; in some areas was also detected basal membrane and an increase in the amount of collagen fibers in the space of Disse; 4) Marked bile canaliculi dilatations with reduction of microvilli and thickening of the pericanalicular surrounding area, some canaliculi were constitued by several hepatocytes. Ductules were found in only 3 cases with the following alterations: 1) Intracytoplasmic electron dense deposits of granular material without limiting membranes; 2) A marked increase in the number of microfilaments mainly located in the apical portion of the cell or in the vicinity of the nuclei; 3) Inflammatory cells in the duct epithelium or in direct contact with the hepatocytes. The ultrastructural findings in the two cases of neonatal hepatitis (NH) resembled those described in the biliary atresia.(ABSTRACT TRUNCATED AT 250 WORDS)