Two rare cases of isolated central nervous system (CNS) candidiasis in preterm infants have been diagnosed in a tertiary neonatal centre over the past 6 years. Despite the life-threatening nature of the disease, biochemical infection markers were not useful for the early identification of localized fungal infection. Because the infection was likely to have been blood borne, we postulated that the initial fungal load was probably low and that the organisms were rapidly eliminated from the circulation after a few had been deposited in the CNS. Hence, the absence of fungaemia or systemic involvement precluded the activation of cytokines and cellular markers. Clinicians should be aware of the limitation of biochemical infection markers so that diagnosis and treatment of fungal infection will not be delayed.