The newborn screening program in Latvia was started in 1980 as pilot study project. Mass screening for phenylketonuria (PKU) in the whole republic was started in 1987, but for congenital hypothyroidism (CH) it begun in 1996. Last two years the Latvian State Medical Genetics Center (SMGC) screened nearly 25,000 newborn dried blood specimens per year. Approximately 25% are repeat and control specimens. Efficiency of the screening program is nearly 97%. Fluorometric method is used for PKU screening, followed by amino acid analysis (HPLC) and analysis of DNA samples for mutations of the PAH gene. Most of the 51 Latvian PKU patients detected from 1980 to 1998 were selected by neonatal screening (38), while the others (13) were diagnosed during genetic counseling. The incidence of PKU in Latvia is 1:8,700 births. CH screening is based on measurement of thyroid stimulating hormone (TSH), using fluoroimmunoassay method, with cut-off value 10 mlU/l, as the primary screening test, and T3 and T4, as confirmatory tests for diagnosis. From 38,684 newborns 37,380 were screened for CH in 1996 and 1997. From these 1,438 (3.8%) newborns were recalled because of initial elevation of TSH level. From these 85 (0.2%) newborns had elevated TSH level during first two weeks of life and were referred to SMGC for repeat testing and follow-up. The diagnosis of CH has been confirmed in 6 babies. The incidence of CH in Latvia is about 1:6,450.