With the continuing increase in the number of severely immunocompromised patients, hospitals are faced with the growing problem of invasive aspergillosis and other opportunistic fungal infections. Since treatment of these infections are difficult and outcome is often fatal, preventive measures are of major importance in the control of invasive filamentous fungal infections. Until recently, inhalation of airborne conidia was believed to be the primary route of acquiring Aspergillus infection. Despite the fact, that efforts to filter the hospital air has led to a reduction of airborne conidia paralleled by a decrease in the frequency of invasive infections, the correlation between the concentration of Aspergillus conidia in hospital air and the risk of invasive infections remains unclear. Furthermore, alternative modes of transmission may exist and should be recognized and investigated. The discovery of hospital water as a potential source of Aspergillus fumigatus and other filamentous fungi may suggest a new route for the transmission of invasive filamentous fungal infections. Epidemiological studies, based on molecular characterization and comparisons of fungal isolates recovered from patients and environment, are needed to expand our understanding of these alternative routes of transmission.