Centrosomes are organelles involved in the organization of the mitotic spindle and may also be the targets of autoantibodies in autoimmune diseases. Human Ninein (hNinein) is a centrosomal autoantigen that is identified by autoimmune patient sera. However, none of the hNinein-specific fragments recognized by the autoantibodies in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) sera have been thoroughly characterized. We thus attempted to identify the fine specificity within the hNinein protein. In this study, four recombinant proteins in two isoforms of hNinein were used as autoantigens along with immunoassays as a molecular tool to investigate the prevalence of hNinein autoreactivity and its specificity in 22 RA and 32 SLE autoimmune disease sera. The data indicated a 50% higher prevalence of isoform 4 hNinein N-terminal autoantibodies in RA sera, whereas 22% of SLE patients were autoreactive to the N-terminal of isoform 4 hNinein compared to only a small percentage of autoreactive normal sera (5%). These results showed that autoepitopes on autoantigen hNinein are restricted to the N-terminal region and that a more significant proportion of RA patients exhibited centrosome reactivity.