The local patterns of fungal isolates were studied by a retrospective analysis of fungal species isolated from clinical specimens in a university hospital in Jerusalem. Between 1984 and 1993, 5630 fungi [4071 patient unique isolates (PUI)] were isolated and identified. During the study decade, the annual incidence of all isolates increased 2.7-fold, and PUI increased 1.6-fold. Candida albicans accounted for 61% of PUI; urine was the source of 53%. The intensive care units (ICUs) and the Bone Marrow Transplantation (BMT) Department had the highest incidence of fungal isolation. The following trends were observed: (1) a decrease in the relative frequency of C. albicans and increase in Candida tropicalis; (2) increased number of isolates from urine, surgical wounds and intra-abdominal sites; (3) increased number of isolates from ICUs and BMT. Fungi are emerging as important hospital-acquired pathogens in tertiary care and teaching hospitals, and are associated with high rates of morbidity and mortality. It is important to be familiar with the local patterns of fungal isolation in order to improve treatment.