The aims of the study were to define the duration of candidaemia in newborn infants and to determine the incidence of persistent hospital-acquired candidaemia and its associated morbidity and mortality compared with non-persistent candidaemia. This retrospective study, included 56 neonates admitted to the neonatal intensive care unit from 1996 to 2000 who had one or more positive blood cultures for Candida spp. The most prevalent pathogen was Candida albicans (64.3%). Mean disease duration was 6.9 ± 5.5 days (median 6 days). Twenty-nine patients (52%) had a positive blood culture for >5 days (persistent candidaemia). There were no statistically significant differences between the infants with persistent and non-persistent candidaemia in background or predisposing clinical factors. Fungal endocarditis was present in four patients (13.7%) with persistent disease and one patient (3.7%) with non-persistent disease (odds ratio 4.19), and uveitis developed in one patient. Ten patients (17.8%) died – five with persistent and five with non-persistent disease (P = 1.0). These findings indicate that persistent neonatal candidaemia may be associated with an increased risk of Candida endocarditis, but not with other complications or increased mortality.