Rheumatoid arthritis is a chronic inflammatory disease characterized by synovial inflammation and pannus formation leading to destruction of cartilage and bone. Several self proteins have been suggested to be disease-driving autoantigens. Proteins are encoded by a limited number of genes in our genome. Post-translational modifications such as citrullination of the arginine residues, can increase the morphological and the functional diversity of the proteome. The positivity of anti-citrullinated peptides autoantibodies occurs then at an early stage of the disease development. Several factors, among which the synovial tissue inflammatory and the nitric oxide reaction, are involved in the regulation of the citrullination reaction. All of them have to be analysed and considered to understand the loss of tolerance and the development of autoimmunity leading to the disease.