Background: Although several countries, including Germany, have established newborn hearing screening programmes for early detection and treatment of newborns with hearing impairments, nationwide tracking systems for follow-up of newborns with positive test results until diagnosis of hearing impairment have often not been implemented. However, a recent study on universal newborn hearing screening in Bavaria showed that, in a high proportion of newborns, early diagnosis was only possible with the use of a tracking system. The aim of this study was, therefore, to assess the cost-effectiveness of tracking newborns with bilateral hearing impairment in Bavaria. Methods: Data from a Bavarian pilot project on newborn hearing screening and Bavarian newborn hearing screening facilities were used to assess the cost-effectiveness of the inclusion of a tracking system within a newborn hearing screening programme. A model-based cost-effectiveness analysis was conducted. The time horizon of the model was limited to the newborn hearing screening programme. Costs of the initial hearing screening test and subsequent tests were included, as well as costs of diagnosis and costs of tracking. The outcome measure of the economic analysis was the cost per case of bilateral hearing impairment detected. In order to reflect uncertainty, deterministic and probabilistic sensitivity analyses were performed. Results: The incremental cost-effectiveness ratio of tracking vs. no tracking was (sic)1,697 per additional case of bilateral hearing impairment detected. Conclusions: Compared with no tracking, tracking resulted in more cases of bilateral hearing impairment detected as well as higher costs. If society is willing to pay at least (sic)1,697 per additional case of bilateral hearing impairment detected, tracking can be recommended.