We retrospectively evaluated autopsy-proven invasive fungal infections (IFIs) in patients with AIDS who died between 1984 and 2002. IFIs were identified in 297 (18.2%) of 1,630 autopsies. Their prevalence significantly decreased over time (from 25.0% in 1984-1988 to 15% in 1998-2002; P = .004), mainly owing to a significant decrease in pneumocystosis (P = .017) and cryptococcosis (P = .003), whereas the prevalence of aspergillosis and histoplasmosis remained relatively stable and of candidiasis and zygomycosis tended to increase in the last years (P = .028 and P = .042, respectively). IFIs were suspected or confirmed during life in only 46.8% of the cases; this proportion did not vary significantly over time (P = .320). The infections contributed to the deaths of 103 patients (34.7%), and their global impact on mortality was 6.3%. Of fatal cases, 38 (36.9%) were characterized by missed antemortem diagnoses, 17 (45%) of which met Goldman criteria for class I errors. The epidemiology of IFIs in patients with AIDS is evolving and not completely mirrored by clinical diagnoses or current diagnostic methods. Our results confirm the valuable role of autopsy data, even with highly effective therapies and advanced technologies.