Invasive pulmonary aspergillosis (IPA) is a frequently fatal infection in immunocompromised patients that is difficult to diagnose. Present methods for detection of Aspergillus spp. in bronchoalveolar lavage (BAL) fluid and in tissue vary in sensitivity and specificity. We therefore developed an A. fumigatus-specific quantitative real-time PCR-based assay utilizing fluorescent resonance energy transfer (FRET) technology. We compared the assay to quantitative culture of BAL fluid and lung tissue in a rabbit model of experimental IPA. Using an enzymatic and high-speed mechanical cell wall disruption protocol, DNA was extracted from samples of BAL fluid and lung tissues from noninfected and A. fumigatus-infected rabbits. A unique primer set amplified internal transcribed spacer regions (ITS) 1 and 2 of the rRNA operon. Amplicon was detected using FRET probes targeting a unique region of ITS1. Quantitation of A. fumigatus DNA was achieved by use of external standards. The presence of PCR inhibitors was determined by use of a unique control plasmid. The analytical sensitivity of the assay was ≤10 copies of target DNA. No cross-reactivity occurred with other medically important filamentous fungi. The assay results correlated with pulmonary fungal burden as determined by quantitative culture (r = 0.72, Spearman rank correlation; P ≤ 0.0001). The mean number of genome equivalents detected in untreated animals was 3.86 log10 (range, 0.86 to 6.39 log10) in tissue. There was a 3.53-log10 mean reduction of A. fumigatus genome equivalents in animals treated with amphotericin B (AMB) (95% confidence interval, 3.38 to 3.69 log10; P ≤ 0.0001), which correlated with the reduction of residual fungal burden in lung tissue measured in terms of log10 CFU/gram. The enhanced quantitative sensitivity of the real-time PCR assay was evidenced by detection of A. fumigatus genome in infarcted culture-negative lobes, by a greater number of mean genome equivalents compared to the number of CFU per gram in tissue and BAL fluid, and by superior detection of therapeutic response to AMB in BAL fluid compared to culture. This real-time PCR assay using FRET technology is highly sensitive and specific in detecting A. fumigatus DNA from BAL fluid and lung tissue in experimental IPA.