Indirect immunofluorescence (IIF) is the main technique for the detection of antinuclear antibodies (ANA) and antineutrophil cytoplasmic antibodies (ANCA). The fully automated IIF processor HELIOS(®) is the first IIF processor that is able to automatically prepare slides and perform automatic reading. The objective of the present study was to determine the diagnostic performance of this system for ANA and ANCA IIF interpretation, in comparison with visual IIF. ANA detection by visual IIF or HELIOS(®) was performed on 425 sera samples including: 218 consecutive samples submitted to a reference laboratory for routine ANA testing, 137 samples from healthy subjects and 70 ANA/ENA positive samples. For ANCA determination, 170 sera samples were collected: 40 samples for routine testing, 90 samples from healthy blood donors and 40 anti-PR3/anti-MPO positive subjects. Good correlation was found for the visual and automated ANA IIF approach regarding positive/negative discrimination of these samples (kappa = 0.633 for ANA positive samples and kappa = 0.657 for ANA negative samples, respectively). Positive/negative IIF ANCA discrimination by HELIOS(®) and visual IIF revealed a complete agreement of 100% in sera from healthy patients and PR3/MPO positive samples (kappa = 1.00). There was 95% agreement between the ANCA IIF performed by automated and visual IIF on the investigation of routine samples. Based on these results, HELIOS(®) demonstrated a high diagnostic performance for the automated ANA and ANCA IIF interpretation that was similar to a visual reading in all groups of samples.