Objectives The objective of this study was to test the hypothesis that patients with primum atrioventricular septal defect (AVSD) have an imbalance in the positions of the left ventricular papillary muscles compared with healthy subjects, and that this anatomic imbalance correlates with left deviation of the QRS axis. Background The function and contraction pattern of the heart is best predicted when cardiac anatomy is considered together with its electrical activation sequence. Understanding the electroanatomic relationships is essential for discovering the developmental relationships between the conduction system and heart structures. Left deviation of the QRS axis is typically present in patients with primum AVSD. However, the pathophysiology of this phenomenon is not understood. Methods Thirty-five patients with primum AVSD and 35 healthy subjects were included in the study. Echocardiographic images were used to determine the papillary muscle positions. A 12-lead electrocardiogram was used to determine the QRS axis in the frontal plane in both patients and healthy subjects. Results An imbalance between papillary muscle positions in primum AVSD patients was defined as the position of the anterior papillary muscle closer to the septum and/or the position of the posterior papillary muscle further from the septum compared with the position of the papillary muscles in healthy subjects. In primum AVSD patients compared with control subjects, there was significant imbalance in the positions of the papillary muscles (p = 0.0007). The imbalance of papillary muscles correlated with deviation of the QRS (r = 0.5, p = 0.0019). Conclusions Abnormality in the position of the papillary muscles changes continuously with the abnormality of the QRS axis. Understanding the electroanatomic relationships provides important insight into developmental relationships between the conduction system and the trabecular structures in primum AVSD patients. These results may provide insights in understanding the continuity of primum AVSD abnormality, in estimating the best surgical approach, and predicting the prognosis of primum AVSD patients.