Invasive aspergillosis (IA) caused by inherently more antifungal-resistant non-fumigatus Aspergillus species has become an important life-threatening complication in severely immunocompromised patients with cancer. The purpose of this study was to compare the relative incidence of, risk factors for, and in vitro correlation of amphotericin B and itraconazole with the clinical outcome of IA caused by Aspergillus fumigatus with those of IA caused by non-fumigatus Aspergillus spp. in patients with cancer. A retrospective search of our tertiary care cancer center's microbiology laboratory reports from 1998-2001 revealed 40 patients with cancer and IA. A non-fumigatus Aspergillus species caused IA in 28 (70%) of those patients. A. fumigatus was the predominant cause of late-onset IA after bone marrow transplantation (p = 0.05), whereas IA due to non-fumigatus Aspergillus spp. was more common in patients with neutropenia (p = 0.01). The minimum inhibitory concentration (50/90) and minimum fungicidal concentration (50/90) for amphotericin B were higher in the non-fumigatus Aspergillus spp. group than in the A. fumigatus one. The Aspergillus species distribution in IA cases in our institution shows a predominance of the more antifungal-resistant or -tolerant non-fumigatus Aspergillus spp.