Objective: We report on a fetus with left atrial isomerism and structural anomalies compatible with heterotaxy syndrome but with a normal karyotype. Case report: A 30-year-old healthy female primigravida with no history of miscarriage or family genetic abnormalities showed low risk for major chromosomal aneuploidies (trisomy 21, 18, and 13) at the combined first-trimester screening. Fetal ultrasound at the 20 th gestational week demonstrated left atrial isomerism, VSD (0.46 mm), morphological right ventricle (left side) connecting to the aorta, morphological left ventricle (right side) connecting to the pulmonary trunk, and infracardiac and supracardiac total anomalous pulmonary venous return. Cytogenetic analysis of amniotic fluid cells by routine karyotyping and array comparative genomic hybridization (aCGH) revealed a normal female fetus. The pregnancy was terminated before the 24th gestational week, and autopsy was performed. Conclusion: Heterotaxy syndrome, a rare congenital anomaly, can present with various clinical manifestations but with a normal karyotype.