To study the new ISPAE guidelines in neonates with congenital hypothyroidism and present authors' experience in managing these neonates. A retrospective review of all babies who were screened for congenital hypothyroidism in the institution over a period of 5 y was conducted. Details pertaining to maternal risk factors, neonatal risk factors, screening TSH, venous TSH and details of etiological evaluation including: ultrasound thyroid, technetium 99m scintigraphy and anti thyroid peroxidase antibody estimation were retrieved. The cases were assessed using the new ISPAE guidelines. During the study period, 8107 babies were screened for congenital hypothyroidism, 83 cases had confirmed disease and 47 had established etiology. There is a fair correlation between screening TSH and venous TSH (r = 0.7, p < 0.05). The estimated incidence of congenital hypothyroidism in present series is 1 in 97 cases. Out of the 83 cases, 36 (43.3%), 16 (19.2%) and 31 (37.3%) cases had screening TSH >20 μIU/mL, 6-20 μIU/mL and < 6 μIU/mL, respectively. Out of the 47 babies with screening TSH <20 μIU/mL, 23 (48.9%), 25 (53.1%) and 12 (25.5%) cases had prematurity, maternal thyroid disease and illness, respectively, as risk factors (some babies had more than one risk factor). Of the 83 cases, all of them had venous TSH >10 μIU/mL and five cases had low Free T4 (<1.1ng/dl). Thus, none of the cases with congenital hypothyroidism were missed on the new ISPAE guidelines. The new ISPAE guidelines for neonatal screening for congenital hypothyroidism are very useful and applicable in Indian neonates.