Congenital heart disease (CHD) is one of the most common organ-specific birth defects and a major cause of infant morbidity and mortality. Despite ultrasound screening guidelines, the detection rate of CHD is limited. Fetal intelligent navigation echocardiography (FINE) has been introduced to extract reference planes and cardiac axis from cardiac spatiotemporal image correlation (STIC) volume datasets. This study analyses the cardiac axis in fetuses affected by CHD/thoracic masses (n = 545) compared to healthy fetuses (n = 1543) generated by FINE. After marking seven anatomical structures, the FINE software generated semi-automatically nine echocardiography standard planes and calculated the cardiac axis. Our study reveals that depending on the type of CHD, the cardiac axis varies. In approximately 86% (471 of 542 volumes) of our pathological cases, an abnormal cardiac axis (normal median = 40-45°) was detectable. Significant differences between the fetal axis of the normal heart versus CHD were detected in HLHS, pulmonary atresia, TOF (p-value < 0.0001), RAA, situs ambiguus (p-value = 0.0001-0.001) and absent pulmonary valve syndrome, DORV, thoracic masses (p-value = 0.001-0.01). This analysis confirms that in fetuses with CHD, the cardiac axis can significantly deviate from the normal range. FINE appears to be a valuable tool to identify cardiac defects.