Introduction: We retrospectively assessed the incidence of congenital hypothyroidism (CH) detected through our neonatal screening program between 1997 and 2010. We describe the diagnostic characteristics of the detected population and verify the impact of a TSH cutoff (CO) change. Patients and Methods: Screening was based on TSH determination on dried blood spot on filter paper samples (IFMA) using a 15 mU/l blood CO until 12/2002 (P1) and 10 mU/l thereafter (P2). Patients were classified as having transient or permanent CH (athyreotic, ectopic, eutopic, with goiter and unknown etiology). Global and diagnostic-related incidences were calculated for the whole studied period with the same CO, and P1 and P2 were compared. Results: Incidences of permanent CH were 1:3,108 (P1) and 1:2,367 (P2). The lower CO detected 22 extra CH, 13 of them definitive (70% with eutopic glands). Only a significant increase (p < 0.05) in eutopic CH was found, partially related to the lower CO applied. A statistically significant association with time was seen for total definitive and ectopic cases (p < 0.05). Conclusion: Our findings revealed some changes in the detected population partially related to the CO applied, with only eutopic dysfunctional disorders being more prevalent in the later years. Total permanent CH and ectopic thyroid disorders showed a trend toward higher detection over time, but their prevalence has not changed significantly in our screening program.