OBJECTIVE: In the development of novel therapies for systemic lupus erythematosus, antinuclear antibody (ANA) positivity represents a criterion for trial eligibility. Since as many as 30% of patients enrolled in trials have been ANA negative, we evaluated the performance characteristics of immunofluorescence assays (IFAs) for ANA determinations for screening. METHODS: This study used 5 commercially available IFAs to assess the ANA status of 181 patients enrolled in a phase II clinical trial for an anti-interleukin-6 antibody. Enrollment included a detailed review of medical records to verify a historical ANA value. IFA results were related to various clinical and serologic features at enrollment. RESULTS: While the frequency of ANA negativity assessed by the central laboratory was 23.8% in a cohort of 181 patients, the evaluated IFA kits demonstrated frequencies of negativity from 0.6 to 27.6%. With 2 IFA kits showing a significant frequency of ANA negativity, positive and negative samples differed in levels of anti-double-stranded DNA, C3, and presence of other ANAs as well as the frequency of high interferon (IFN) expression. CONCLUSION: These findings indicate that, when used for screening, IFAs can vary because of performance characteristics of kits and thus can affect determination of trial eligibility. With kits producing a significant frequency of ANA negativity, ANA status can be associated with other serologic measures as well as the presence of the IFN signature, potentially affecting responsiveness to a trial agent.