A cohort study of candidemia and central venous catheters (CVC) was conducted in infants in a neonatal intensive care unit over a 5 year period (1994-1998). There were 104 cases of candidemia with CVCs included in the study. There were 73 peripheral CVCs, 28 surgical CVCs, and 6 umbilical CVCs. The timing of CVC removal was at the discretion of the attending neonatologists. All infants were treated with Amphotericin B. Fifty infants had early-removal of CVCs [ER-CVC] (within 3 days of first positive blood culture for Candida sp.), and 54 infants had late removal of CVCs [LR-CVC] (>3 days). Both ER-CVC and LR-CVC infants had similar severity of illness as measured by the National Therapeutic Intervention Scoring system scores. ER-CVC infants had significantly shorter duration of candidemia with a median of 3 days (range 1-14) compared to LR-CVC infants with a median of 6 days (range 1-24 days), p=0.0002. The timing of CVC removal had no impact of case fatality rate with C. parapsilosis candidemia: 1 of 26 (4%) died in the ER-CVC group and 1 of 28 (4%) died in the LR-CVC group. The case fatality rate from C. albicans candidemia was significantly affected by timing of CVC removal: 0 of 21 infants died in the ER-CVC group in contrast to 9 of 23 (39%) infants in the LR-CVC group, p=0.002, odds ratio 28.2. Failure to remove central venous catheters as soon as candidemia was detected in neonates was associated with increased mortality in C. albicans candidemia, and prolonged duration of candidemia regardless of Candida species.