The etiology of congenital hypothyroidism (CH) may play an important role in determining disease severity, outcome, and, therefore, its treatment schedule. Radionuclide imaging (RI) is currently the most precise diagnostic technique to establish the etiology of CH. Conventional ultrasound can identify an athyrotic condition at the normal neck position and has gained acceptance for the initial evaluation of CH; however, its ability in delineating ectopic thyroid is limited. We used color Doppler ultrasonography (CDU) to assess blood flow and morphology in the detection of ectopic thyroid in 11 CH patients disclosed by neonatal screening; thyroid glands were undetectable at the normal location by gray-scale ultrasonography (GSU). The patients studied consisted of two infants for initial investigation and nine children for reevaluating the cause of CH. All of the patients underwent GSU, CDU, RI, and magnetic resonance imaging (MRI) investigation. We set RI as the defining diagnostic test for detecting ectopic thyroid and compared the imaging of CDU with those of GSU and MRI. The results of RI showed 10 ectopic thyroids and one athyreosis. In the patients with ectopic thyroid, the sensitivity of CDU, GSU, and MRI for detecting ectopic thyroid was 90, 70, and 70%, respectively. We conclude that CDU is superior to GSU and MRI for detecting ectopic thyroid and that CDU may be adopted as the diagnostic tool for the initial investigation of suspected CH.