Background: Patients who develop fungal infections are reported to have increased hospital admissions, lengths of stay, cost, and higher mortality rates compared to non-infected patients.  The frequency and spectrum of fungi is changing.  Trends suggest fungi other than Aspergillus and Candida, in particular non-albicans Candida, have become increasingly common.  To better understand the changing epidemiology, we implemented a fungal pathogen surveillance system at an academic medical center.    Methods:  Isolates of fungal pathogens from January to December 2003 were extracted from the laboratory reporting system and entered into a surveillance database.  Data were collated and analyzed by species, unit, site and date of first isolation.   Results: Preliminary data on 827 first isolates of fungal pathogens, from 700 patients, suggest that Candida species were the most common 94.1% (n=778), followed by Aspergillus species 4.2% (n=35).  Thirty two percent were non-albicans canidida species.  A predominance of Candida albicans was seen in the unit specific analysis, ranging from 50% in the bone marrow transplant unit (BMTU) to 70% in the surgical intensive care unit (SICU).  Among Aspergillus, A. fumigatus (51.4%) and A. niger (28.6%) were predominant.  The majority of isolates appear to have been collected from non-significant sites.   Conclusions: While difficult to draw conclusions from one year of data, fungal pathogen surveillance programs can provide incidence data for fungal pathogens, and have the ability to track changes in the spectrum.  This data can be provided to clinicians to direct prevention and treatment strategies.