Background: The purpose of the study was to: 1) investigate carotid atherosclerotic plaque morphology and immunohistochemistry (IHC) with respect to the localization sites of Chlamydia pneumoniae, 2) find correlations between plaque morphology and clinical sonographical characteristics, and 3) determine the correlation between abundance of C. pneumoniae and complexity of the plaque. Materials/Methods: 200 patients with asymptomatic (A = 59) and symptomatic (S = 141) courses of carotid stenosis admitted to the Neurology and Neurosurgery Clinic for TIA or acute ischemic stroke were studied. For IHC the atherosclerotic plaques were incubated with primarily monoclonal anti-Chlamydia pneumoniae antibody clone RP402, code no. M6600, diluted 1:50 (DAKO). Statistical evaluation was performed. Results: 34 (17%) homogeneous (HO), or stable, and 166 (83%) heterogeneous (HE), Or unstable, plaques were divided into 3 HO and 5 HE subtypes according to the number of histopathological signs and prevalence of inflammatory cell types, having different sonographical characteristics and plaque thickness. Complex plaques of both A and S patients have activation signs for chronic inflammation, phagocytosis, and atheromatosis: all three of these in HE plaque subtypes, and only for atheromatosis in HO plaques. Conclusion: 1) C. pneumoniae IHC signals were found in every kind of phagocyte (histiocytes, macrophages, foreign body macrophages, foam cells, PMNs) located in the fibrous cap, atheroma (necrotic core), and especially at tire boundary of fibrous cap/atheroma; 2) complexities were found, so plaque instability signs strongly correlate with abundance of C. pneumoniae (p < 0.001); 3) sufficient correlation between plaque thickness and disease symptomaticity (p < 0.01) was found.