Atrial fibrillation (AF) leads to remodeling characterized by changes in both size and shape of the left atrium (LA). Here we aimed to study the effect of hypertrophic cardiomyopathy (HCM) on the pattern of LA remodeling in AF-patients. HCM-patients (n = 23) undergoing AF ablation (2009–2012) were matched and compared with 125 Non-HCM patients from our prospective registry. Pre-procedural CT data were analyzed (EnSite Verismo, SJM, MN) to determine the maximal sagittal (anterior–posterior, AP), coronal (superior-inferior, SI and transversal, TV) dimensions and the sphericity index (LAS). Volume (LAV) was rendered after appendage (LAA) and pulmonary vein (PV) exclusion. A cutting plane, between PV ostia/LAA and parallel to the posterior wall, divided LAV into anterior- (LAA) and posterior-LA (LAP) parts. The ratio LA-A/LAV was defined as asymmetry index (ASI). HCM patients had a wider inter-ventricular septum and a smaller LV than Non-HCM patients. LA volume (LAV 166 ± 72 vs. 130 ± 36 ml, p = 0.03) and LA diameters were significantly larger in HCM patients. Anterior volume (LA-A: 112 ± 48 vs. 83 ± 26 ml, p < 0.001) differed significantly between groups, whereas the posterior volume LA-P (55 ± 28 vs. 47 ± 13 ml, p = 0.23) and LAS (75% vs. 78%, p = 0.089) was similar in both groups. As a result, ASI was significantly higher (67 ± 6 vs. 63 ± 6%, p = 0.01) in HCM than in Non-HCM patients. In conclusion, LA remodeling in patients with AF and HCM is characterized by asymmetric dilatation, driven by an anterior rather than a posterior dilatation. This can be characterized by three-dimensional imaging and could be used as surrogate of advanced atrial remodeling.