The hemodynamics after Fontan surgery are notable for hypertension and dilation of the right atrium (RA). The effect of this stress on atrial cytoarchitecture has not been systematically studied and might be relevant to arrhythmias and their treatment. Morphologic and histopathologic analyses were performed on tissue from the RA and left atrium (LA) from autopsy specimens of Fontan hearts (n = 47). The findings were compared to those from control samples from young patients with normal atrial hemodynamics (n = 15). Most Fontan specimens were from young patients who died after a relatively short duration of Fontan physiology. The tissues were analyzed for wall thickness, fibrosis content, and fibrosis pattern. The mean wall thickness for the RA (3.0 +/- 1.0 mm) and LA (2.3 +/- 0.6 mm) in the Fontan hearts was significantly greater than that in the control hearts (RA, 1.8 +/- 0.4 mm; LA, 1.8 +/- 0.5 mm; p <0.001 and p = 0.024, respectively). The predictors for thickening of the RA included (1) older age at Fontan surgery, (2) older age at death, and (3) longer duration of Fontan circulation. The Fontan hearts and control hearts exhibited nearly identical fibrosis patterns in the RA and LA. Neither wall thickness nor fibrosis varied with the 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 the Fontan atria; however, because a similar pattern was present in the control tissue, this likely represented normal fibroelastic atrial structure, rather than a specific response to Fontan hemodynamics. The degree of wall thickening observed in the Fontan atria was not so excessive as to preclude transmural lesions during catheter or surgical ablation of reentrant arrhythmias.