Aims: The aims of this study are to investigate the incidence and determinants of post-operative atrial arrhythmias, conduction disorders and mortality in hypertrophic obstructive cardiomyopathy (HOCM) patients undergoing transaortic myectomy. Methods and results: This retrospective single-center study was conducted in 249 patients (median age 54 years [40–64], 42% female) undergoing transaortic myectomy. Post-operative atrial fibrillation (AF) was reported in 84 patients (33.7%), including 56 patients (22.5%) with de novo AF. Older age (HR = 1.027 (1.003–1.052), p = 0.029) and hypercholesterolemia (HR = 2.296 (1.091–4.832) p = 0.029) were independent predictors for de novo post-operative AF. Late post-operative AF and atrial flutter (AFL) occurred in 18.9% and 6.8% of the patients, respectively. De novo early post-operative AF increased the risk of late post-operative AF (HR = 3.138 (1.450–6.789), p = 0.004). Patients with a right bundle branch block had a higher risk of early-postoperative pacemaker implantation (p = 0.003, HR = 9.771 (2.195–43.505)). Higher age at time of surgery (HR = 1.053 (1.026–1.081), p < 0.001) was a predictor for late mortality (n = 47, 18.9%). Conclusion: Early and late post-operative AF, AFL and other SVTs are common sequelae after myectomy and are associated with older age at surgery, history of AF and early post-operative AF. Early post-operative arrhythmias are not transient and periodic rhythm monitoring is therefore essential to initiate therapy as soon as possible.