Background Antibodies to citrullinated proteins have been described in patients with RA and these appear to be the most specific markers of the disease. The objective of this study was to analyse the improvement in diagnostic accuracy of anti-cyclic citrullinated peptide autoantibodies and IgA rheumatoid factor in patients with clinical suspicion of RA and who were IgM rheumatoid factor-positive. Anti-CCP antibodies were measured with three different second-generation enzyme immunoassays. Methods We chose 133 serum samples with IgM RF levels greater than 20 IU/mL sent to our Laboratory from Specialized Care Units. Subsequently, patients were classified according to their clinical records. Eighty-seven had rheumatoid arthritis and 46 had other diseases. In all samples anti-CCP and IgA RF were measured by the corresponding ELISAs. Results Comparison of the three anti-CCP second-generation ELISAs revealed differences between them. Likewise, clinical performances in terms of sensitivity, specificity, and positive and negative likelihood ratios were different. In patients with IgM RF higher than 20 IU/mL, anti-CCP antibodies increased the clinical efficiency of IgM RF and offered better performance as compared with IgA RF. Conclusions The use of anti-CCP antibodies affords good clinical efficiency and modifies the pre-test probability of the occurrence of RA in patients with IgM rheumatoid factor higher than 20 IU/mL.