Guidelines emphasize that the appropriate time frame for neonatal screening with the heel stick test is from the 3rd to 7th day of life, in 100% of newborns. Treatment for congenital hypothyroidism and phenylketonuria, when initiated in the first two weeks of life, is capable of preventing the neurological sequelae of these diseases. The Rio de Janeiro State Neonatal Screening Program was accredited for Phase 2 of the National Neonatal Screening Program, with two program models (A and B). A performance analysis was conducted for the Neonatal Screening Program, for the years 2005 to 2007. Coverage increased from 2002 to 2007, reaching 80.4%, with 33.8% of the blood samples drawn in the first 7 days of life. The two models showed similar performance, short of the targets, with 50% of the confirmed cases receiving their diagnosis at more than 48 days of life. The delays accumulated in the various stages of the process can impede the benefits of early detection, the cornerstone of neonatal screening. The deleterious long-term effects transcend the individual sphere, with an impact on the health system and a major social burden.