Objective: Study on genetic variation of foot-and-mouth disease (FMD) virus, the causetive agent of FMD outbreaks in Iran. Design: Case study. Animals: The tongue and mouth epithelial lesions of 11 clinical livestock suspected to FMD from 9 outbreaks during S eptember, 2002. Procedures: Total extracted RNAs were used in diagnostic one step RT-PCR. VP1 gene from positive samples was then amplified in the multiplex RT-PCR for current types viral isolates in Iran. The PCR products were sequenced using fluorescent dye deoxy-terminator cycle sequencing. Results: Nine of the era mined samples out of whole were positive for FMD viral genome. Except the samples of type A, which both samples were from an outbreak in Isfahan, all of the positive samples were type O. The Considerable variation revealed in amino acids sequences of type A sample. Conclusion: Results of this study shows evolution of a new genetic variant. However, serological and crossneutralization assays are required for confirming the antigenic diversity.