A rapid and simple homogeneous fluorescence PCR assay was developed for the clinical diagnosis of infectious diseases based on a molecular beacon. The established method could reproducibly detect Mycobacterium tuberculosis at the 10 bacteria/mL level. The analytical specificity was tested with 14 strains of mycobacterium, four unrelated bacteria and 220 negative samples; no false positive results were obtained. A blind test was also performed to evaluate its performance in Mycobacterium tuberculosis diagnosis. The results showed that both the clinical sensitivity and the specificity were 100%, and that the detection limit was in the range of 1-10 bacteria/ml. A clinical study with 466 patient samples demonstrated that fluorescence PCR assay correlated well with smear (93.6%) and culture (98.4%) methods for positive samples. However, fluorescence PCR could detect positive samples (62.9%) more than smear (30.3%) and culture (31.4%), indicating a higher sensitivity of the present method than the traditional ones. The feasibility of this method was further approved by successful detection of Neisseria gonorrhoeae and Chlamydia trachomatis.