Right atrial (RA) size is a prognostic indicator for heart failure and cardiovascular death in adults. Data regarding use of RA area (RAA) by two-dimensional echocardiography as a surrogate for RA size and allometric modeling to define appropriate indexing of the RAA are lacking. Our objective was to validate RAA as a reliable measure of RA size and to define normal reference values by transthoracic echocardiography (TTE) in a large population of healthy children and develop Z-scores using a validated allometric model for indexing RAA independent of age, sex, and body size. Agreement between RAA and volume by 2D, 3D TTE, and MRI was assessed. RAA not volume by 2D TTE is an excellent surrogate for RA size. RAA/BSA¹ has an inverse correlation with BSA with a residual relationship to BSA (r = − 0.54, p < 0.0001). The allometric exponent (AE) derived for the entire cohort (0.85) also fails to eliminate the residual relationship. The entire cohort divided into two groups with a BSA cut-off of 1 m² to provide the best-fit allometric model (r = 0). The AE by least square regression analysis for each group is 0.95 and 0.88 for BSA < 1 m² and > 1 m², respectively, and was validated against an independent sample. The mean indexed RAA ± SD for BSA ≤ 1 m² and > 1 m² is 9.7 ± 1.3 cm² and 8.7 ± 1.3 cm², respectively, and was used to derive Z-scores. RAA by 2D TTE is superior to 2D or 3D echocardiography-derived RA volume as a measure of RA size using CMR as the reference standard. RAA when indexed to BSA¹, decreases as body size increases. The best-fit allometric modeling is used to create Z scores. RAA/BSA^0.95 for BSA < 1 m² and RAA/BSA^0.88 for those with BSA > 1 m² can be used to derive Z scores.