Hepatic fibrosis is an important complication after Fontan surgery in patients with single-ventricle congenital heart disease. Few reports of hepatic histology in these patients exist, and sinusoidal fibrosis has been described. We aimed to characterize fibrosis at liver biopsy procedure in patients with previous Fontan surgery and to identify patient variables associated with the degree of fibrosis. All patients who had previous Fontan surgery and who subsequently underwent liver biopsy at our institution between January 1990 and July 2010 were identified. For each biopsy specimen, portal and sinusoidal fibrosis were graded and medical records reviewed. Biopsy specimens from 13 patients were examined; the median time from Fontan surgery to liver biopsy procedure was 16.9 years (range 6.9–25). At the most recent biopsy procedure, 12 patients (92 %) had evidence of portal fibrosis, including 1 patient with portal-based cirrhosis. Thirteen patients (100 %) had at least some degree of sinusoidal fibrosis, including 1 patient with centrilobular-based cirrhosis. Lower platelet count was associated with greater degree of portal fibrosis by ordinal regression (odds ratio 0.84, P = 0.04), and patients with no or mild portal fibrosis had significantly higher platelet counts compared with those with moderate or severe portal disease (278 ± 78 K vs. 160 ± 46 K, P = 0.005). Four patients underwent serial biopsy procedures; portal fibrosis was progressed in 3 patients, and sinusoidal fibrosis was progressed in 3 patients. After Fontan surgery, portal and sinusoidal fibrosis are common at liver biopsy and can progress over time. Lower platelet count may represent a marker of portal-based disease in these patients.