An outbreak of Nipah virus infection occurred in 1998 in Malaysia in which a total of more than 1 million pigs were culled and 109 people died from this disease. Samples were collected from frugivorous bats living in Malaysia that were considered to be a natural reservoir of Nipah virus. There were two kinds of fruit bats, the so-called flying fox and the small fruit bat. Samples were collected from small fruit bats and flying foxes caught by mist net traps. No antibody and no Nipah virus were detected from the samples of small fruit bat. However, an average 18% and 63% positive for antibody were detected from the samples of flying foxes living in the islands (Island flying fox) and peninsula of Malaysia (Malayan flying fox), respectively. Nipah virus was not isolated from either of the flying foxes. However, Nipah virus gene was detected from Malayan flying fox by real-time PCR. Reovirus like virus and other unknown viruses were isolated from Malayan flying foxes. From these results, flying fox was an important natural reservoir of Nipah virus and especially Malayan flying fox was considered to be more important as a natural reservoir.