A polymerase chain reaction (PCR) method was developed for detecting measles virus (MV) RNA in a variety of clinical samples using primer pairs in the nucleocapsid (N) and matrix (M) genes in one reaction (dual target-PCR). The dual target-PCR detected MV RNA in tissue culture fluid containing 1 TCID50 of the MV Loss strain, and was as sensitive as a single target-PCR. Specificity was confirmed by the failure of the dual target-PCR to amplify products from the infected tissue culture containing related paramyxoviruses. Thirty-two of 35 (91.4%) samples collected from 23 patients with confirmed measles infection by the detection of measles specific IgM were found to be positive for MV RNA by PCR. Direct sequencing of the PCR amplicons revealed three different genotypes among the MV strains that were detected in 12 patients. The dual target-PCR method is suitable for the diagnosis of measles infection and, based on the sequencing of the PCR product DNA, for investigating the molecular epidemiology of MV strains.