To assess whether invasive aspergillosis (IA) was hospital acquired, Aspergillus fumigatus isolates, obtained during a one-year study from inpatients with haematological diseases and IA and from their environment, were genotyped using microsatellite markers. The analysis of 62 environmental isolates showed an extremely diverse A. fumigatus population with 43 genotypes represented only once. Eight genotypes were found more than twice at different times and/or at different locations showing that a given isolate can persist over time and is not dependent on a specific location. Twenty-seven isolates were obtained from 12 patients with IA. Of eight patients with multiple isolates, four were infected with isolates of different genotypes. Five patients (42%) had hospital-acquired IA according to the following definitions: patients infected with an isolate found in the environment, or patients infected with the same genotype. Although genotyping results are highly suggestive of hospital-acquired IA, this cannot be proved definitively because of the high diversity of the A. fumigatus population and the limited environmental sampling. A better knowledge of the A. fumigatus population outside hospitals is needed. For this purpose, genotyping using microsatellite markers seems appropriate.