We evaluated the utility of HEp-2 cells transfected with the 60 kDa SS-A/Ro as a substrate for indirect immunofluorescence (IIF-HEp-2000) to compare several methods for screening Japanese serum samples for anti-SS-A/Ro antibodies. Serum samples from 243 Japanese patients were analyzed by IIF for anti-nuclear antibodies (ANAs), using HEp-2 cells (IIF-HEp-2), and for anti-SS-A/Ro 60 kDa antibodies, using IIF-HEp-2000 and enzyme-linked immunosorbent assay (ELISA). We performed double immunodiffusion and immunoprecipitation experiments, using the products of in vitro transcription and translation, to analyze sera for which there were discrepancies in the results of the IIF-HEp-2000 assay and ELISA. A total of 93 of the 243 serum samples showed findings positive for anti-SS-A/Ro antibodies. Notably, eight of the 93 sera gave positive findings for anti-SS-A/Ro antibodies by IIF-HEp-2000 but ANA-negative by IIF-HEp-2 analysis. Seven sera possessing anti-SS-A/Ro antibodies gave false negative results by IIF-HEp-2000; however, those samples were all ANA positive. ELISA for anti-SS-A/Ro antibodies showed that five and two samples gave false positive and negative results, respectively. Analysis by IIF-HEp-2000 was useful for primary screening of patients for ANAs, especially for anti-SS-A/Ro antibodies; the test could detect anti-SS-A/Ro antibodies not identified on standard substrates in samples obtained from the Japanese population, as reported for the Caucasian population.