The present survey in Austria, Germany and Switzerland continued the survey of cryptococcosis set up by the European Confederation of Medical Mycology (ECMM) in 1997. From 2000 to 2003 77 cases have been reported. An HIV infection is still the most important risk factor (68%). Young HIV+ women from ASIA contributed to the increase of cryptococcosis in females. A total of 129 clinical isolates of both surveys were genotyped by PCR fingerprinting to study the prevalence of different genotypes. The prevalence of Cryptococcus neoformans var. grubii (serotype A) with the genotypes VNA1 and VNA2 was higher in Germany and Austria (74.5%) than in Switzerland (52%), while in Switzerland the Cr. neoformans hybrids AD (26%) and Cr. neoformans var. neoformans (serotype D) (22%) were more prevalent compared with Germany and Austria (8 and 17.5% respectively). Cryptococcus gattii isolates were studied by FT-IR spectroscopy. DNA in the ITS region was sequenced to get further information about Cr. neoformans serotype AD strains and about the geographical origin of the Cr. gattii isolates. The ITS sequence of the serotype AD isolates of the genotypes VNAD1, VNAD2 and VNAD4 is usually identical to serotype A or serotype D respectively. In the three isolates of the genotype VNAD3 a genotype-specific sequence pattern was detected. Two autochthonous infections due to Cr. gattii could indicate that the genotype VGIV with the ITS type 'Asia 2' might be endemic in Europe.