Objective: The Fontan operation greatly improves survival for single ventricle congenital heart disease patients but creates a physiology that leads to long-term multi-organ dysfunction. A non-invasive screening tool that can identify impending decline is sought. The objective of this pilot study was to assess the microcirculation in Fontan-palliated patients by measuring tissue oxygen saturation (StO2) in superficial and deeper tissues. Approach: Three patient cohorts were studied: Fontan group (n = 8) and two patient control groups, liver disease group (n = 8) and tetralogy of Fallot group (n = 9). 22 healthy controls were also examined. Superficial and deeper StO2 was measured at the forearm, thenar eminence, index and ring fingers of both arms using the LEA O2C spectrophotometry device. Main results: Superficial StO2 was reduced in Fontan patients compared to healthy controls (p = 0.002) and tetralogy patients (p = 0.016), but not compared to the liver group (p = 0.313). Deeper StO2 was similar between groups (p = 0.112). The gap between deeper and superficial StO2 was raised in Fontan patients compared to healthy controls (p = 0.001) and tetralogy patients (p = 0.037), but not compared to the liver group (p = 0.504). There was no clinically relevant difference in StO2 between the left and right arms, and the variation in StO2 according to measurement site was similar between the four groups. Significance: Vascular optical spectrophotometry is a feasible non-invasive measure of micro-circulatory function that can easily be performed in the clinic setting and may have utility in patients with Fontan circulations. Further, we provide important normal range data in the healthy control population which can be used to design future studies.