Hemodynamics following Fontan surgery are notable for right atrial (RA) hypertension and dilation. The effect of this stress on atrial cytoarchitecture has not been studied systematically, and may be relevant to arrhythmias and their treatment. Morphologic and histopathologic analysis was performed on RA and left atrial (LA) tissue from post-mortem specimens of Fontan hearts (n = 47) and compared to control samples from young patients with normal atrial hemodynamics (n = 15). Most Fontan specimens were from young patients who expired after a relatively short duration of Fontan physiology. Tissues were analyzed for wall thickness, fibrosis content, and fibrosis pattern. Mean wall thickness for both RA (3.0±1.0 mm) and LA (2.3±0.6 mm) in Fontan hearts was significantly greater than in control hearts (RA = 1.8±0.4 mm and LA = 1.8±0.5 mm, p<0.001 and p=0.024, respectively). Predictors for RA thickening included: a) older age at Fontan surgery, b) older age at death, and c) longer duration of Fontan circulation. Fontan hearts and controls exhibited nearly identical RA and LA fibrosis patterns. Neither wall thickness nor fibrosis varied with underlying heart defect or style of Fontan connection. In conclusion, atrial remodeling after Fontan surgery for univentricular heart physiology involves increased wall thickness in both the RA and LA. Interstitial fibrosis was also observed in Fontan atria, but because a similar pattern was present in control tissue, this likely represents normal fibroelastic atrial structure rather than a specific response to Fontan hemodynamics. The degree of wall thickening observed in Fontan atria was not so excessive as to preclude transmural lesions during catheter or surgical ablation of reentrant arrhythmias.