Molecular mimicry is one of the most important pathogenic factor of microorganism and is defined as a structural similarity of microbial molecules to host tissue contributing to the pathogenicity. Mimicry can be observed at the molecular, serological and functional level. In the review the infectious diseases have been discussed where the mimicry phenomenon may occur, and also autoimmune disease where due to the molecular mimicry bacterial structures are potent to induce adverse immune reactions. The cross-reacting molecules mimicking the host structures comprise colominic acid, sialic acid containing capsular polysaccharides of Streptococcus group B, phosphocholine containing antigen, lipopolysaccharides of Campylobacter jejuni contributing in induction of Guillain-Barré syndrome or Lewis antigen containing lipopolysaccharides of Helicobacter pylori inducing gut carcinoma. Knowledge on the phenomenon of molecular mimicry is important when new conjugate vaccine has to be constructed, because great care should be paid not to induce autoantibodies with synthetic immunogen. Investigation of microbial factors reveal that many autoimmune diseases are of infection etiology.