Nasopharyngeal carcinomas (NPC) are epithelial neoplasms which show a distinct geographical distribution and have a characteristic histology. These tumors have multifactorial etiology, including virological, environmental, and genetic components. The aim of the present study is to assess the relation between Epstein-Barr-virus (EBV) and subtypes of NPC in Aegean Turkish patients. In the present study, nasopharyngeal biopsies of 84 cases diagnosed as nasopharyngeal carcinoma, between 1998 and 2004, were reevaluated. In situ hybridization with the fluorescein-conjugated EBV-encoded small nuclear RNA (EBER) oligonucleotide probe was performed on paraffin-embedded tissue sections using an automated slide stainer system. Of 84 patients, 55 were men and 29 were women with ages ranging between 7 and 77 years (median 50, mean 46.73). Seventy-three of 84 cases were EBER positive. All of 62 cases (100.0%) with undifferentiated carcinoma, 8 of 16 (50.0%) with differentiated nonkeratinizing carcinoma, and three of six (50.0%) with keratinizing squamous cell carcinoma were EBV positive. EBER positivity was statistically significantly higher in undifferentiated carcinomas, compared to the other morphological subtypes (p = 0.000). Our results showed that all morphological subtypes of NPC are highly associated with EBV latent infection in our region, and a higher prevalence was found for the undifferentiated subtype.