Background Atrial fibrillation (AF) is the most common preoperative arrhythmia in heart valve surgery patients and its prevalence is rising. This study aims to investigate the impact of AF on valve surgery early complications and survival and on valve disease of different aetiologies and populations with particular reference to Indigenous Australians with rheumatic heart disease (RHD). Methods The Australian and New Zealand Society of Cardiac and Thoracic Surgeons Cardiac Surgery Database was analysed to determine the association between preoperative AF and valve surgery outcome. Its association with demographics, co-morbidities, preoperative status and short and long term outcome was assessed. Results Outcome of 1594 RHD and 19,029 non-RHD-related surgical procedures was analysed. Patients with preoperative AF were more likely to be older, female, Indigenous, to have RHD and to bear a greater burden of comorbidities. Patients with RHD and preoperative AF had a longer hospital stay and were more likely to require reoperation. Adjusted short (OR 1.4, 95% CI 1.2–1.7) and long term (HR 1.5, 95% CI 1.3–1.7) survival was inferior for patients with non-RHD preoperative AF but was no different for Indigenous and non-Indigenous Australians with RHD. Conclusions In this prospective Australian study, patients with valve disease and preoperative AF had inferior short and long term survival. This was particularly the case for patients with non-RHD valve disease. Earlier intervention or more aggressive AF management should be investigated as mechanisms for enhancing postoperative outcomes. This may influence treatment choice and the need for ongoing anticoagulation.