Purpose: The current Joint Committee on Infant Hearing guidelines recommend that infants with syndromes or craniofacial abnormalities (CFAs) who pass the universal newborn hearing screening (UNHS) undergo audiological assessment by 9 months of age. However, emerging research suggests that children with these risk factors are at increased risk of early hearing loss despite passing UNHS. To establish whether earlier diagnostic audiological assessment is warranted for all infants with a syndrome or CFA, regardless of screening outcome, this study compared audiological outcomes of those who passed UNHS and those who referred. Method: A retrospective analysis was performed on infants with a syndrome or CFA born between July 1, 2012, and June 30, 2017 who participated in Queensland, Australia's state-wide UNHS program. Results: Permanent childhood hearing loss (PCHL) yield was higher among infants who referred on newborn hearing screening (51.20%) than in those who passed. Nonetheless, 27.47% of infants who passed were subsequently diagnosed with hearing loss (4.45% PCHL, 23.02% transient conductive), but PCHL was generally milder in this cohort. After microtia/atresia, the most common PCHL etiologies were Trisomy 21, other syndromes, and cleft palate. Of the other syndromes, Pierre Robin sequence featured prominently among infants who passed the hearing screen and were subsequently diagnosed with PCHL, whereas there was a broader mix of other syndromes that caused PCHL in infants who referred on screening. Conclusion: Children identified with a syndrome or CFA benefit from early diagnostic audiological assessment, regardless of their newborn hearing screening outcome.