Summary Head and Neck Cancer (HNC) has been studied in different regions of the world but little is known about its incidence patterns in the Middle East and Egypt. In this study from Egypt’s only population-based registry, we analyzed data from 1999-2006, to estimate incidence, incidence rate ratios (IRRs) and 95% confidence intervals (CIs) categorized by age, district and subsites. Overall urban incidence of HNC was twice or more that of rural incidence for both males (IRR = 2.59; 95% CI = 2.26, 2.97) and females (IRR = 2.00; 95% CI = 1.64, 2.43). Highest urban-rural difference for males was seen in 40-49 years (IRR = 2.79; 95% CI = 1.92, 4.05) and for females in 30-39 years (IRR = 2.94; 95% CI = 1.60, 5.40). Among subsites, highest incidence among males was for larynx (1.53/105) and among females for gum and mouth (0.48/105). Maximum urban-rural difference in males was for paranasal sinus (IRR = 4.66; 95% CI = 1.88, 11.54) and in females for lip (IRR = 8.91; 95% CI = 1.89, 41.98). The study underscores the patterns of HNC incidence in Egypt while indicating the need for future analytical studies investigating specific risk factors of HNC in this population.