In line with global progress towards early detection of permanent congenital and early-onset hearing loss (PCEHL), the costs and performance of hospital-based and community-based infant hearing screening models were evaluated in Lagos, Nigeria. The protocol consisted of two-stage screening with transient-evoked otoacoustic emissions and automated auditory brainstem response followed by diagnostic evaluation for all infants referred after the second-stage screening. The main outcome measures were referral rates at screening, cost per baby screened, cost per case detected and yield for PCEHL. First-stage referrals were 32.2% for universal and 31.7% for targeted screening in the hospital, compared with 14.3% and 15.2%, respectively for the community-based programme. Second-stage referrals ranged from 3.3% under hospital-based universal screening to 4.9% under community-based targeted screening. The highest yields of 27.4 and 22.5 per 1000 were recorded under community-based targeted and universal screening, respectively. Screening cost per child was lowest (US$7.62) under community-based universal screening and highest (US$73.24) under hospital-based targeted screening. Similarly, cost per child detected with PCEHL was lowest (US$602.49) for community-based universal screening and highest (US$4631.33) for hospital-based targeted screening. Community-based universal screening of infants during routine immunisation clinics appears to be the most cost-effective model for early detection of PCEHL in low-income countries.