A study of epidemic transmission of Chikungunya virus (CHIK) was initiated in April 1999 in Yogyakarta, Indonesia. Three hundred seventeen volunteers from three kelurahans (sub-districts) were recruited. Anti-CHIK IgG antibodies were detected in 68% to 74% of cases and 28% to 32% of controls. In the kelurahan with no reported CHIK illness, 29% of cases and 28% of controls had anti-CHIK IgG antibodies. None of these cases demonstrated anti-CHIK IgM antibodies. In the two kelurahans with disease activity, anti-CHIK IgM antibodies were detected in 3% to 36% of cases, with the highest percentage from the kelurahan with recently reported cases. Ten percent of controls from Gowok had anti-CHIK IgM detected in their serum. Twelve acutely ill volunteers were later included from the kelurahan Pilahan for virus identification. Samples from two volunteers were culture- and RT-PCR-positive for CHIK. This is the first documentation of epidemic transmission of CHIK in Indonesia since 1982.