Abstract: Background and Objectives: Subclinical and overt hypothyroidism represent major health problems with an increasing prevalence and a potential serious impact on mother health. It affects the measurement of nuchal translucency to the degree that forced the obstetricians to re-evaluate it as a single screening test for aneuploidies and encouraged them toward the use of other maternal serum markers early in pregnancy. To clarify the effect of subclinical hypothyroidism on the interpretation of nuchal Translucency in early pregnancy. Materials and Methods: A prospective comparative case control study was conducted at the out patients clinic of the Obstetrical Department at Al-Yarmouk Teaching Hospital from the 1st of September 2016 to the 1st of September 2018. About 140 pregnant women were enrolled in the study; 100 of them were apparently healthy pregnant women in their first trimester (11-13+6 weeks) assigned as a control group and the other 40 were pregnant women of the same gestational age diagnosed as having subclinical hypothyroidism after thyroid function screening of 500 pregnant women who attended this tertiary hospital and were assigned as patient group. Ultrasound measurement of the crown ramp length and nuchal translucency had been done for all participants. The data from both groups were statistically analyzed and compared. Results: Forty patients had subclinical hypothyroidism from a total of 500 women screened (8%). The mean measurement of nuchal translucency was significantly higher in the patient group compared to control group (2.92±0.96 versus 2.45±0.62 mm, respectively) and there was a significant positive linear correlation between nuchal translucency (NT) and thyroid stimulating hormone (TSH) level. All those with abnormally raised nuchal translucency delivered healthy fetuses. Conclusion: Subclinical hypothyroidism might affect the interpretation of nuchal translucency and reduce its significance as a screening test in that population.