The aye-aye (Daubentonia madagascariensis) is an unusual lemur with a small population in human care. Cardiac pathologies, but not normal size parameters, have been reported in this species. This study aimed to determine whether radiographic cardiac scaling systems commonly used to evaluate heart size in domestic mammals have potential clinical application in aye-ayes. Selected cardiac silhouette, vertebral, and intrathoracic skeletal dimensions were measured retrospectively on paired sets of orthogonal thoracic radiographs collected during health examinations of aye-ayes maintained at three British zoos. Measurements from 21 healthy aye-ayes (10 males, 11 females) of varying ages were used to calculate reference intervals (RI) with 90% confidence intervals for vertebral heart scale in both right lateral (VHS-RLat) and ventrodorsal (VHS-VD) projections, a modified VHS (VHS-Mod), thoracic inlet heart size (TIHS), and cardiothoracic ratio (CTR). VHS-VD (9.49 ± 0.29) was slightly higher than VHS-RLat (9.32 ± 0.33; P = 0.08) and had the lowest coefficient of variation of the scaling indices; TIHS was 4.89 ± 0.36, VHS-Mod was 11.07 ± 0.49, and CTR was 0.53 ± 0.05. Thoracic depth-to-width ratio of aye-ayes ranged between 0.75 and 0.91, equivalent to an intermediate thoracic morphology in dogs. No scaling indices differed significantly by sex, age group, or thoracic morphology; however, VHS-Mod and CTR were significantly correlated with bodyweight (P = 0.0022 and P = 0.041, respectively) and CTR with age (P = 0.02). Summed cardiac dimensions demonstrated a near-linear relationship with bodyweight and T4 vertebral length (both P < 0.05), but not thoracic inlet length (P = 0.12). Analysis of measurements by using serial radiographs from hand-reared animals indicated potential utility of RI in aye-ayes >0.4 yr. Overall, results suggest VHS-VD and VHS-RLat are preferred cardiac scaling indices in aye-ayes. These data will aid zoo clinicians in the evaluation of cardiac size and identification of cardiomegaly in this endangered primate.