Mycoplasma hyopneumoniae is an important cause of pneumonia in pigs around the world, but confirming its presence in (or absence from) pigs can be difficult. Culture for diagnosis is impractical, and seroconversion is often delayed after natural infection, limiting the use of serology. Numerous PCR assays for the detection of M. hyopneumoniae have been developed, targeting several different genes. Recently, genetic diversity among strains of M. hyopneumoniae was demonstrated. The effect of this diversity on the accuracy and sensitivity of the M. hyopneumoniae PCR assays could result in false-negative results in current PCR tests. In this study, a panel of isolates of M. hyopneumoniae, M. flocculare, M. hyorhinis, and M. hyosynoviae were tested with a number of M. hyopneumoniae-specific PCR assays. Some M. hyopneumoniae PCR assays tested did not detect all isolates of M. hyopneumoniae. To increase the efficiency of PCR testing, two new real-time PCR assays that are specific and capable of detecting all of the M. hyopneumoniae isolates used in this study were developed.Mycoplasma hyopneumoniae is the causative agent of enzootic pneumonia and an integral component of the porcine respiratory disease complex. Considered one of the most important sources of disease-associated losses in swine production, M. hyopneumoniae is also one of the most difficult to detect. This organism is difficult to isolate in pure culture because it is easily overgrown by other contaminating bacteria; therefore, culture is generally not attempted. In addition, seroconversion to M. hyopneumoniae is often slow within a herd and can vary considerably among pigs, making the use of enzyme-linked immunosorbent assays less effective. A number of PCR assays have been developed and reported to be both sensitive and specific for M. hyopneumoniae (4,6,11,19,20,22,24,26). As a result, this technique is now among the most widely used for detection of M. hyopneumoniae in pigs.While the development of PCR assays has greatly enhanced our ability to detect M. hyopneumoniae, the genetic variability of the organism (1,5,12,14,15,21) can affect detection by PCR. It is not known what effect this heterogeneity has on the sensitivities of the different assays. Real-time PCR has many advantages over traditional PCR assays, including less time to obtain quantitative results and a decrease in environmental contamination. Together, these traits make real-time PCR assays preferred in diagnostic and research settings. A real-time assay that is based on a conserved target common among isolates of M. hyopneumoniae has not yet been described. The two currently published M. hyopneumoniae-specific real-time assays had to be used in combination in order to detect all M.hyopneumoniae field samples in a Swiss collection of isolates (6). In addition, many of the previously published PCR assays were validated using only a small number of mycoplasma isolates. Therefore, the objectives of this study were to measure the ability of several M. hyopneumoniae-specific PCR assays to de...