Chlamydia pneumoniae (C. p.) is an intracellular parasite directly involved in respiratory disease and more recently in chronic degenerative pathologies as atherosclerosis and asthma. Its peculiar life cycle makes cultural isolation difficult, thus, troublesome the diagnosis of the disease. Serology is so far the most common method of diagnosis of the, although the indirect based evidence of the serology may give clinically misleading results. Nucleic acid amplification methods offer indeed rapid, reliable and low cost assessment pathogen bacteria isolation, with relevant benefits for the patient's management. These molecular methods are nowadays essential in presence of bacteria of difficult cultivation or method inconsistent with temporal clinical needs, for they allow to rapidly detect even nucleic acid traces of the infectious agent, providing direct evidence of its presence in the biological samples and hence the relevant therapy. Nucleic acid methods are extensively applied in laboratory diagnosis of Chlamydia trachomatis bringing about the development of sensitive and reliable commercial kits. This review analyses the literature of the genic amplification methods in the search of C. p. in clinical samples highlighting methodological and diagnostic aspects. Although genic amplification methods have been implemented presently by the clinical research labs only, it is anticipated that through their standardisation they could be used by most clinical microbiology laboratories.