A PCR system was developed that allowed recognition of three major pathogenic Aspergillus species, namely A. fumigatus, A. niger and A. flavus, in isolates obtained from clinical specimens. The primer pair for PCR was designed from conserved sequences of internal transcribed spacer 1 (ITS1) ribosomal DNA and its flanking regions. Products 521 bp in size were successfully amplified by PCR from the seven Aspergillus species most frequently encountered as opportunistic pathogens, and the three most commonly significant species were identified by separate PCR reactions or nested PCR based on use of species-specific primers. To our knowledge, this is first report of identification of the second and third most frequent pathogenic Aspergillus species using specific PCR amplification. The PCR based identification system reported here will be a powerful tool to control difficult pulmonary fungal infections and to speed the application of effective treatment.