We designed and implemented a detailed dose-estimating algorithm for cardiac C-arm CT (3DRA), based on the PCXMC software application for single shot x-ray dose calculation. 3DRA is associated with overall effective doses of 5.5 ± 1.4 mSv (ICRP 60) to 6.6 ± 1.8 mSv (ICRP 103). The need for 3D cardiac reconstruction depends on medical judgement, weighing benefits against radiation dose. However, the effective dose of 3DRA compares favourably to conventional cardiac CT. Moreover, per-ablation imaging has many logistical and image integration advantages. Manual collimation by the operator can reduce effective dose by more than 20% and is therefore imperative. BMI is the only reliable predictor of effective dose for the evaluated system. The effective dose paradoxically decreases for increasing patient calibre due to the system’s technical specifications. Unfortunately, no simple dose conversion coefficient based on DAP values is possible for current 3DRA.