A study was conducted to measure the prevalence of hemagglutination-inhibition (HI) and neutralizing antibodies against two arboviruses (Chikungunya and Japanese encephalitis virus) in horses of Java, Indonesia. Blood specimens were collected from a sample of 112 horses at two stables: Pulo Mas, a racing track-horse complex, located in a residential area in North Jakarta, and Pamulang, a riding school, located in a rural environment of West Jaya. Sera were tested by the HI assay and plaque reduction neutralization test. JEV antibodies were detected by HI in 58 (52%) of the horses, while only 11 (10%) had Chikungunya antibodies by HI. The proportion of Pamulang horses infected with JEV (66%) was significantly higher than found among Pulo Mas horses (40%) screened (p < 0.01). Of the 58 horses with JEV antibodies by HI, 52 (90%) were found to have specific neutralization antibodies to JEV. HI and neutralization tests on horse sera indicated that the risk to alpha virus infections was minimal in horses surveyed from Java. However, there was a high risk of JEV infection among the same population.