Mycoplasma gallisepticum- or M. synoviae-challenged chickens were monitored with serological assays (serum plate agglutination, hemagglutination inhibition, and enzyme-linked immunosorbent assay) and polymerase chain reaction (PCR). The tracheal swabs from M. gallisepticum-challenged chickens received three different treatments (phosphate-buffered saline [PBS], Frey's broth, or 10 mM Tris-HCl/250 mM ethylenediaminetetraacetic acid/ 2.5% sodium dodecyl sulfate [STE]) prior to DNA purification. A nonphenolic method for DNA extraction was utilized. The best PCR results were obtained with PBS swab treatment. The nonphenolic method for DNA extraction was compared with a phenolic method in an experiment with tracheal swabs from M. synoviae-challenged chickens and commercial flocks. Both methods gave comparable results.