Background Invasive fungal infections have constituted an increasingly important cause of morbidity and mortality in immunocompromised patients. In this study, a surveillance project was conducted in three different intensive care units of two large tertiary hospitals in China.Methods A one-year surveillance project was conducted in two tertiary hospitals which located in north China and southwest China respectively. Air, surfaces and tap water were sampled twice a month in a central intensive care unit, a bone marrow transplant unit, a neurosurgery intensive care unit and a live transplant department. Environmental conditions such as humidity, temperature and events taking place, for example the present of the visitors, healthcare staff and cleaning crew were also recorded at the time of sampling.Results The air fungal load was 91.94 cfu/m3 and 71.02 cfu/m3 in the southwest China hospital and the north China hospital respectively. The five most prevalent fungi collected from air and surfaces were Penicillium spp., Cladospcrium spp., Altemaria spp., Aspergillus spp. and Saccharomyces spp. in the southwest China hospital, meanwhile Penicillium spp., Fusarium spp., Aspergillus spp., Altemaria spp. and Cladospcrium spp. in the north China hospital. The least contaminated department was intensive care units, and the heaviest contaminated department was neurosurgery intensive care unit. Seventy-three percent of all surfaces examined in the north China hospital and eighty-six percent in the southwest China hospital yielded fungi. Fifty-four percent of water samples from the north China hospital and forty-nine percent from the southwest China hospital yielded fungi.Conclusions These findings suggested that the fungus exist in the environment of the hospital including air, surface and water. Air and surface fungal load fluctuated over the year. Air fungal load was lower in winter and higher In summer and autumn, but seldom exceeded acceptable level. The higher values were created during May to August in the north China hospital and May to June and September to October in the southwest China hospital. A correlation between air fungal load and humidity, as well as personnel was observed.