It has been demonstrated that hepatic apparent diffusion coefficients (ADC) are decreasing in patients with a Fontan circulation. It remains however unclear whether this is a true decrease of molecular diffusion, or rather reflects decreased microperfusion due to decreased portal blood flow. The purpose of this study was therefore to differentiate diffusion and microperfusion using intravoxel incoherent motion (IVIM) modeled diffusion-weighted imaging (DWI) for different liver segments in patients with a Fontan circulation, compare to a control group, and relate with liver function, chronic hepatic congestion and hepatic disease. For that purpose, livers of 59 consecutively included patients with Fontan circulation (29 men; mean-age, 19.1 years) were examined (Oct 2012─Dec 2013) with 1.5T MRI and DWI (b = 0,50,100,250,500,750,1500,1750 s/mm2). IVIM (Dslow, Dfast, ffast) and ADC were calculated for eight liver segments, compared to a control group (19 volunteers; 10 men; mean-age, 32.9 years), and correlated to follow-up duration, clinical variables, and laboratory measurements associated with liver function. The results demonstrated that microperfusion was reduced (p<0.001) in Fontan livers compared to controls with ─38.1% for Dfast and ─32.6% for ffast. Molecular diffusion (Dslow) was similar between patients and controls, while ADC was significantly lower (─14.3%) in patients (p<0.001). ADC decreased significantly with follow-up duration after Fontan operation (r = ─0.657). Dslow showed significant inverse correlations (r = ─0.591) with follow-up duration whereas Dfast and ffast did not. From these results it was concluded that the decreasing ADC values in Fontan livers compared with controls reflect decreases in hepatic microperfusion rather than any change in molecular diffusion. However, with the time elapsed since the Fontan operation molecular diffusion and ADC decreased while microperfusion remained stable. This indicates that after Fontan operation initial blood flow effects on the liver are followed by intracellular changes preceding the formation of fibrosis and cirrhosis.