Background: There are currently no guidelines concerning additional laboratory testing for specific autoantibodies among anti-nuclear antibody-negative sera with an anti-cytoplasmic staining pattern identified by indirect immunofluorescence assay. Moreover, few data are available that address this laboratory situation. Methods: We performed specific autoantibody assays in 200 sera with an anti-nuclear antibody titer <= 1: 32 and a cytoplasmic titer (undefined staining pattern) of >= 1: 64, identified sequentially in the course of routine anti-nuclear antibody testing. Results: A total of 85 sera (42.5%) were positive in one (n=57) or more (n=28) of the specific autoantibody tests performed. Autoantibodies identified were antimitochondrial (15%), anti-microsomal (13%), anti-neutrophil cytoplasmic (10%), anti-smooth muscle (6%), anti-parietal cell (4%), and extractable nuclear antigen (8.5%, including histones, SSA, SSB, Sm, Jo-1 or Scl-70). A positive result in one or more of these assays was more frequent at anti-cytoplasmic titers >= 1:1024 (77.8%) than at titers of 1:64-1:128 (7%) (chi(2) = 25.3, p < 0.001). Conclusions: The present data demonstrate that undefined anti-cytoplasmic staining in anti-nuclear antibody-negative sera is associated with, although not necessarily caused by, a high frequency and wide range of specific autoantibodies. Further work is needed before specific recommendations can be made concerning follow-up in subjects with this laboratory finding.