Aim: Targeted screening by a salivary cytomegalovirus (CMV) polymerase chain reaction (PCR) of infants who ‘refer’ on their newborn hearing screen has been suggested as an easy, reliable and cost-effective approach to identify and treat babies with congenital CMV (cCMV) to improve hearing outcomes. This study aimed to investigate the feasibility and cost-effectiveness of introducing targeted salivary cCMV testing into a newborn hearing screening programme. Methods: The study included three tertiary maternity hospitals in Queensland, Australia between August 2014 and April 2016. Infants who ‘referred’ on the newborn hearing screen were offered a salivary swab for CMV PCR at the point of referral to audiology. Swabs were routinely processed and tested for CMV DNA by real-time quantitative PCR. Parents of babies with a positive CMV PCR were notified, and the babies were medically assessed and, where appropriate, were offered treatment (oral valganciclovir). Results: Of eligible infants, the parents of 83.0% (234/283) consented to the cCMV screen. Of these, 96.6% returned a negative result (226/234), and 3.4% (8/234) returned a positive result (three true positive; five false positive). The prevalence of cCMV for infants with confirmed hearing loss was 3.64% (P = 2/55; confidence interval = 0.44–12.53%). The cost comparison suggests the cost implementation of cCMV screening (and subsequent potential treatment benefits and management over time), compared to non-screening (and subsequent management), to be negligible. Conclusion: Incorporating cCMV testing into Universal Newborn Hearing Screening within Queensland is realistic and achievable, both practically and financially.