Background: Congenital hypothyroidism (CH) is a common and preventable cause of intellectual disability for which early diagnosis is difficult without newborn screening. Genetic and environmental factors, race, ethnicity, sex, and pregnancy outcomes were noted as risk factors. In the study we aimed to determine the incidence of CH among different ethnic groups in the capital of Macedoina - a multiethnic city. Methods: A 14-year retrospective cohort analysis was performed on 121,507 newborns in the capital of Macedonia, Skopje, screened for whole-blood thyroid-stimulating hormone (TSH), in dry blood spots collected 48-72 h after birth, during the period 2002-2015. A TSH value of 15 mIU/L was used as cutoff point until 2010 and 10 mIU/L thereafter. Results: Primary CH was detected in 46 newborns (female to male ratio 1.3) with overall incidence of 3.8/10,000 (1/2641). The incidence of primary CH was significantly increased after lowering the TSH cutoff value (p = 0.038), primarily due to detected neonates with transient CH for this period. Ethnic differences in the incidence of primary CH were detected. CH incidence among Roma neonates (6.7/10,000) was significantly higher (p < 0.05) than the incidence detected in Macedonians (3.9/10,000) or Albanians (3.7/10,000). Conclusions: Increased incidence of CH in Roma newborns was detected as compared to other ethnicities in the capital of Macedonia. Further analysis of factors in direct interrelationship with the increased CH incidence in Roma newborns, as well as elucidation of impact of the CH incidence in this ethnicity on the overall incidence in Skopje, is warranted.