Although an association between Chlamydia pneumoniae (Cpn) or Cytomegalovirus (CMV) infection and coronary atherosclerosis has been reported, such an association is less clear for acute coronary syndromes (ACS). The purpose of this study was to investigate the pathogenic roles of Cpn and CMV infection of coronary plaques in ACS. We divided 38 coronary plaque specimens obtained from 38 patients who underwent directional coronary atherectomy or thrombectomy into an ACS group (n = 21) and a non-ACS group (n = 17). Cpn and CMV in specimens were stained using immunohistochemical techniques and analyzed quantitatively. The detection rate for either Cpn- or CMV-positive cells in ACS patients was slightly higher compared with non-ACS patients. Detection rates for both Cpn- and CMV-positive cells were significantly higher in ACS patients than in non-ACS patients (P = 0.010). Furthermore, the density of Cpn- and CMV-positive cells in plaques was significantly higher in ACS patients than in non-ACS patients (P < 0.003). The results indicate that the presence and severity of Cpn and CMV infection in coronary plaques are greater in patients with ACS compared with non-ACS patients. We conclude that infection with Cpn and CMV in coronary plaques may be involved in the pathogenesis of ACS.