Citrullinated peptides in autoimmune diseases have been extensively studied in the last two decades. It is suggested that citrullination and the anti-citrullinated peptide antibodies (ACPA) plays a critical role in initiating inflammatory responses in autoimmune diseases, such as rheumatoid arthritis (RA). The most commonly accepted molecular mechanism for citrullinated peptides/proteins in RA is that the modified antigen resulting from cell damage or uncontrolled apoptosis could evoke an immune response leading to autoantibodies against these peptide or the whole protein. Citrullination of arginine is catalyzed by the enzyme peptidylarginine-deiminase (PAD) in the presence of calcium, changing the positively charged arginine to a polar but neutral citrulline. These citrullinated peptides/proteins and the relevant antibodies (ACPA) are important, not only in initiation of RA, but also in the diagnosis of the disease. In this evidence-based clinical review, we summarize recently published data on peptide citrullination and ACPA gauging the ability of anti-cyclic citrullinated peptide (anti-CCP) antibodies for diagnosis of RA. We also recapitulate results of studies elucidating the mechanism underlying the disease.