Peste des petits ruminants (PPR) is an economically important contagious disease of small ruminants. PCR-based techniques have been successfully used for rapid diagnosis of PPR. The method used for isolation of RNA from tissue samples is an important concern when using reverse transcription-PCR (RT-PCR) methods for the detection of PPR virus (PPRV). In this study, a commercial kit for manual preparation and an automated processing technique for RNA extraction were compared in terms of performance. Thirty-two small ruminants, each from different flocks, with PPR suspect submitted to laboratory were chosen to compare manual and automated extraction methods for the detection of PPRV. Vero cells were used for PPRV isolation. One-step RT-PCR was used for the detection of PPRV RNA. From the 32 submitted samples, CPE was observed in 11 samples. PPRV nucleic acid was detected in 11 of 32 samples that were manually extracted, while viral RNA was detected in 9 of 32 extracts prepared by the robot. Two samples that were negative with automated extraction were weakly positive in manual extraction. RNA quality and quantity were assessed using a spectrophotometer. According to the results, difference in quantity among two methods was statistically significant (P<0.0001, two-tailed paired t-test), and manual extraction method is suitable for detection of low amounts of PPRV RNA in clinical samples.