Objectives: To determine the incidence and risk factors of hearing loss (HL) in Brazilian neonates. Study design: 11,900 neonates were screened for hearing and congenital CMV (cCMV). Low and high-risk babies who did not pass their hearing screening and infants with cCMV were scheduled for a diagnostic audiologic evaluation. Results: The incidence of HL was 2 per 1000 live-born infants (95% CI: 1–3). HL was higher in high-risk neonates than in low risk babies (18.6 vs. 0.3/1000 live births, respectively). Among infants exposed to isolated risk factors, association of HL with craniofacial abnormalities/syndromes (RR = 24.47; 95% CI: 5.9–100.9) and cCMV (RR = 9.54; 95% CI: 3.3–27.7) were observed. HL was 20 to 100-fold more likely in neonates exposed to ototoxic drugs in combination with cCMV or craniofacial/congenital anomalies. Conclusions: Strategies for the prevention of cCMV and exposure to ototoxic drugs may decrease the incidence of HL in this population.