Objective To investigate the bacteroides of patients with AIDS and the healthy control by real-time quantitative PCR in order to reveal the role and significance of gut microflora in the AIDS-associated molecular pathogenesis. Methods The feces of the preoperative AIDS patients (n = 30) and the healthy control (n = 30) were collected. According to the sequences of target genes, specific PCR primers were designed. Bacterial genome DNA extracted from fecal samples was quantified by real-time quantitative PCR to analyze the bacterial amounts. Results In the patients with AIDS, the level of B.fragilis (3.23 ± 1.59; 4.05 ± 1.65), B.uniformis (5.69 ± 0.95;6.70 ± 2.18), B.thetaiotaomicron (5.01 ± 1.61; 6.41 ± 2.34), B.ovatus (5.78 ± 1.03; 7.07 ± 1.75), B.distasonis (4.21 ± 1.21; 5.53 ± 2.46) and B.vulgatus (2.92 ± 1.30; 4.48 ± 1.32) were significantly higher than those of healthy controls (P < 0.05). Conclusion The amount of fecal bacteroides of AIDS patients are significantly higher than those of the healthy control. These data indicate that the gut microflora of AIDS patients was disordered.