OBJECTIVE To compare indirect immunofluorescence assay (IIFA) and enzyme-linked immunosorbent assay (ELISA) for detecting antinuclear antibodies (ANA) and anti-double-stranded DNA antibodies (anti-dsDNA). METHODS A total of 125 serum samples were obtained from patients with established or suspected autoimmune disease, and 82 samples were used for ANA detection and 57 for anti-dsDNA detection using both IIFA and ELISA. Fourteen samples were examined for both ANA and anti-dsDNA. In cases where discrepancy occurred in the results by the two methods, extractable nuclear antigens were detected using immunoblotting. RESULTS The positivity rate of ANA detected by IIFA and ELISA was significantly different (87.8% and 73.17%, respectively, P<0.01), but the positivity rate of anti-dsDNA was similar between IIFA and ELISA (77.19% and 71.93%, respectively, P>0.05). The percent agreement between the two testing methods with different cutoff values of ANA and anti-dsDNA showed significant differences (P<0.01), and for some uncommon patterns, the percent agreement of the two methods was lowered in ANA detection but remained unchanged for anti-dsDNA with different ANA patterns. High percent agreements of the two methods were obtained with the cutoff ANA titer of 1:100 and the cutoff anti-dsDNA value of weak positivity, but they demonstrated a significant difference in testing low-titer ANA and anti-dsDNA. CONCLUSIONS IIFA is more sensitive than ELISA in detecting the total ANA and anti-dsDNA. ELISA prescreening combined with IIFA can obtain the information of the nuclear pattern and allow the observation of the titer alterations. The combination of two or more testing methods can greatly enhance the accuracy of the results.