Evoked otoacoustic emissions using click stimulus (cEOEs) were recorded in 450 consecutive children over a 12-month period. Of this group, 102 were babies treated in neonatal intensive care unit (NICU), classified as High Risk neonates according to the criteria of the Joint Committee on Infant Hearing. Audiologic examination in the latter was completed by auditory brainstem responses (ABR). Two of the neonates showed a profound hearing loss accompanied by strong cEOEs. The two cases are described and discussed together with the possibilities and limitations of transient evoked otoacoustic emissions in the auditory screening of the neonatal population. Despite the reported rare possibility of pure retrocochlear disorders, when cEOEs are used for neonatal screening purposes there is an actual risk of missing a profound hearing loss. Nevertheless, the use of cEOEs in combination with ABR may contribute to the differential diagnosis between cochlear and retrocochlear lesions.