Abstract: The invention features methods that are capable of detecting single target molecules in a sample input volume of, e.g., 5 ?l, and of quantifying organismal, e.g., chiamydial, DNA. Desirably, these methods employ a single tube format coupled with fluorescent detection of amplicons. This approach facilitates the application of quantitative PCR (qPCR) to microbiological diagnosis in clinical settings. The invention also features primers and probes for the detection of Chlamydia. The use of specific hybridization probes with qPCR amplification provides the ability for identification of individual species or strains of microorganisms.