Background: The prognosis for pulmonary atresia and intact ventricular septum (PAIVS) has been poor. Our hypothesis is that intrinsic abnormal left ventricular (LV) intramyocardial circulation might be related to the poor outcomes of these patients. Methods:Neonatal heart specimens were examined microscopically in four groups of 6 cases each. Group I had PAIVS with ventriculocoronary artery connections (VCAC), group II had PAIVS without VCAC, group III had normal hearts, and group IV had LV hypertrophy. A projection microscope with grid overlay was used to count the LV intramyocardial coronary artery density (IMCAD), which was expressed as the number of profiles/mm<sup>2</sup>. Results: The LV IMCAD of groups I (0.40 ± 0.14/mm<sup>2</sup>) and II (0.45 ± 0.15/mm<sup>2</sup>) were significantly lower than those of groups III (0.77 ± 0.11/mm<sup>2</sup>) and IV (0.76 ± 0.09/mm<sup>2</sup>; all with p = 0.002). There was no significant difference between either groups I and II (p = 0.394) or groups III and IV (p = 0.818). Conclusions: This study demonstrates lower LV IMCAD in a widely heterogeneous spectrum of neonatal hearts with PAIVS, which might potentially predispose these patients to myocardial ischemia and in turn contribute to the poor prognosis of this disease.