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Tumor marker carbohydrate antigen 19-9 (CA 19-9) level has gained clinical significance in gastrointestinal malignancies and in various solid and cystic diseases. Dysplastic kidney is a congenital abnormality resulting from atresia of the ureteral bud during the embryogenesis which can be unilateral or bilateral. We report unilateral dysplastic kidney with extremely large cyst diagnosed by routine ultrasonography in the 32nd week of gestational age with high levels of CA 19-9 in cystic and amniotic fluid, as well as persistent high urinary levels of this tumor marker during the 1-year follow-up. Persistent high urinary CA 19-9 level even after cyst aspiration may be attributable to remained function of dysplastic kidney due to remained epithelial lining.