For the implementation of the neonatal screening program, the following factors have to be considered for the selection of conditions to be screened and evaluation of outcome. These include the factors pertaining to public health impact, availability and acceptability of the screening system, and other social issues involved in the implementation. In the context of Hong Kong, Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency and Congenital Hypothyroidism (CHT) have been highlighted in the early 1980s for consideration. A territory wide program for screening these conditions was started in 1984. Since then, over 99% of all newborns in Hong Kong was screened. Of these, around 70% were delivered in public hospitals, and the remaining were from private hospitals. Pre-screening education was emphasized, and 95% of pregnant ladies received information about this screening program from the Maternity and Child Health Centers run by the Department of Health, Hong Kong. For those who were born in public hospitals, the incidence of CHT was 1 in 2404 (269/646,580), while that of G6PD deficiency was 4.5% in male newborns and 0.3% in female newborns. This paper highlights details of the screening program, including its outcome evaluation. In Macau, CHT screening has not been started. Instead, G6PD deficiency screening commenced in 1977 in one of the two major hospitals where most newborns are delivered. Methodology and results of this program are presented.