OBJECTIVE The purpose of this review is to summarize recent information that has had a significant impact on the laboratory diagnosis and clinical management of newborns with congenital hypothyroidism and congenital adrenal hyperplasia (CAH). RESULTS An approximate doubling of the incidence rate of congenital hypothyroidism in many parts of the world has been attributed to increased detection of infants with mild disease, delayed thyroid stimulating hormone elevations and demographic changes. A substantial number of children with modest thyroid stimulating hormone elevations on screening have permanent disease. Circulating levels of thyroxine may vary among hypothyroid children who are given identical dosages of medication. Treated infants should be monitored every 1-2 months during the first year of life. Although, generic and brand name thyroxine preparations may not be bioequivalent, children can be well controlled on generic formulations.Enzyme linked immunoassay assay for 17-hydroxyprogesterone is associated with a high rate of false positive specimens. In attempts to minimize this problem, some programs have resorted to two-tier screening of the initial specimen with steroid profiling as the second tier. Several programs are routinely testing second specimens in an effort to reduce the incidence of missed CAH cases. CONCLUSIONS This review explains the uptick in incidence rate of congenital hypothyroidism and underscores issues in management that can affect developmental outcome. One specimen two-tier testing for CAH resulted in an increased false negative rate without significantly reducing the false positive rate. The benefit of collecting second specimens for CAH screening is problematic. Optimal treatment of CAH continues to pose a challenge.