BACKGROUND Portal cavernoma cholangiopathy (PCC), a surgical-endoscopic dilemma, has not been studied comprehensively, more so in children. Our study aimed to evaluate PCC in children using a combination of magnetic resonance cholangiography-portovenography (MRC-MRPV) and endoscopic ultrasonography (EUS). METHODS In this prospective cross-sectional study, recruited children with extrahepatic portal venous obstruction (EHPVO) underwent MRC-MRPV and radial array EUS. PCC was categorized as asymptomatic PCC, symptomatic and no-PCC. Modified Llop grading was used to grade the MRC changes. RESULTS Sixty-six of 72 (92%) children had PCC (85% asymptomatic; 7% symptomatic) on MRC. Age at study and duration of disease had significant correlation (r = 0.588, P < 0.001). 63% had grade III MRC changes. MRC grades and superior mesenteric vein block (64%) on MRPV significantly corresponded with EUS changes (intracholedochal varices, choledochal perforators, intramural cholecystic collaterals and biliary calculi). Superior mesenteric vein non-patency was a strong predictor of MRC biliary changes (P = 0.003, odds ratio 46.4, 95% confidence interval 4.91-623.6). CONCLUSIONS A majority of EHPVO children have asymptomatic cholangiopathy and should be routinely evaluated for PCC at the time of first presentation by MRC-MRPV. Additional superior mesenteric vein block with portal cavernoma results in significantly higher changes of cholangiopathy on MRC and EUS.