Background: The Fontan circulation is associated with low skeletal muscle mass, which affects the accuracy of creatinine-based glomerular filtration rate estimates (eGFR/GFR). Cystatin C, another filtration marker, is less impacted by muscle mass. We examined associations between characteristics of individuals with a Fontan circulation and both creatinine-based and cystatin C-based eGFR. Methods and results: This single-center retrospective study included 107 individuals with a Fontan circulation who had clinical measurements of serum cystatin C and creatinine. GFR was estimated using different equations for adults (≥19 years of age, Chronic Kidney Disease-Epidemiology Collaboration equations for both creatinine and cystatin C) and children (