Human papillomavirus (HPV-16) E6 proteins inhibit apoptosis in both p53-dependent and p53-independent manners. So it was relevant to assess the impact of such infection on head and neck cancers and its relation to the inhibitors of apoptosis (IAPs). CIAP2 is one of these IAPs that is postulated to upregulated by E6 proteins of HPV-16 by amplification of the locus bearing it in many tissues. In this study, we aimed to search for the amplification of the locus bearing CIAP-2 and its relation to HPV-16 in head and neck cancer that may have prognostic and therapeutic impacts on these patients. Total 30 patients diagnosed as head and neck cancer (2 tissue samples were taken from each patient: from the tumor and from the safety margin). All samples were subjected to qualitative polymerase chain reaction analysis for HPV-16 and qualitative and semiquantitative reverse transcription polymerase chain reaction of CIAP-2. There was a significant association between HPV-16 and CIAP2 positivity and head and neck tumors (P=0.01). CIAP-2 expression in malignant tissues was highly associated with HPV-16 infection with 73.9% sensitivity and absolute specificity.