Background: Maternal thyroid disorders during pregnancy can significantly impact fetal development and increase the risk of adverse pregnancy outcomes, including miscarriage, preterm birth, low birth weight, and neonatal morbidity and mortality. This study aims to evaluate the prevalence of thyroid dysfunction in a cohort of 300 neonates (aged 1-28 days) at a tertiary care centre, with a focus on comparing the thyroid hormone levels between neonates born to mothers with and without thyroid disorders. Methods: This was a prospective, observational study conducted over a 12- month period. The neonates were further divided into two groups based on maternal thyroid status: (i) cases (N=150) and (ii) controls (n=150). In the first and third postnatal weeks, the study group's infants' thyroid tests were measured. Results: The mean TSH levels were significantly higher in neonates of mothers with thyroid disorders, while the mean free T4 level was significantly lower in this group. The prevalence of subclinical hypothyroidism (elevated TSH with normal free T4) was significantly higher. Conclusions: Early identification and management of thyroid disorders in newborns can help prevent the adverse effects on growth and neurodevelopment.