Our purpose was to evaluate a two-stage newborn hearing screening program using automated auditory brainstem response (AABR) before discharge and to describe our follow-up program. This study used 4085 infants born in the Seirei-Hamamatsu and Mikatahara General Hospitals during a 2-year period. The initial screening test was performed 2 or 3 days after birth at an intensity of 35 dBnHL. For the infants who were referred from this test, the re-screening test was performed 5 or 6 days after birth. Diagnostic work-up with auditory brainstem response (ABR), otoacoustic emissions (OAE), and a conditioned orientation reflex audiometry (COR) test were performed by the age of 3-6 months. The referral rate was 1.20% (49/4085 infants) in the first test and 0.71% (29/4085 infants) in the two-stage screening. The two-stage screening procedure was able to reduce the false-positive rate from 0.83 to 0.34%. The incidence of bilateral and unilateral congenital hearing loss diagnosed by ABR was 8/4085 (0.20%) infants and 7/4085 (0.17%) infants, respectively. One infant with congenital cytomegalovirus infection, who passed the two-stage AABR tests, was diagnosed with hearing loss 1 month after birth, using ABR. The two-stage measurement of AABR is effective and time efficient due to significant decreases in the referral rate and the false-positive rate.