We discuss the methodological advantages of using X-ray computed tomography (CT) for diagnosing chronic maxillary sinusitis (CMS) of various etiologies on skeletal samples. A CT examination of 20 crania from the Pucará de Tilcara fortress, Argentina (late 8th to 16th centuries AD), was carried out. Criteria for identifying CMS included osteitic lesions in the form of focal destruction, and thickened and sclerotized walls of maxillary sinuses. To determine the etiology of the disease, a tomographic and macroscopic examination of the dentition and bones of the ostiomeatal complex were performed, the presence or absence of facial injuries was assessed, and the co-occurrence of various pathologies was statistically evaluated. Five cases of CMS were identified. Four of these may be of odontogenic origin; in two cases, a secondary infection of the maxillary sinuses is possible. In one instance, the etiology was not determined. No indications of traumatic infection were found. Statistical analysis revealed a relationship of CMS with apical periodontitis and the ante-mortem loss of upper molars and premolars. An indirect symptom of CMS may be the remodeled bone tissue and porosity of the posterior surface of the maxilla.