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The Egyptian Ministry of Health and Population surveillance system provides data about notifiable communicable diseases. This study aimed to provide information for decision-making to reduce the burden of communicable diseases in Egypt by analysis of the surveillance data for 2006-2013 to identify trends in the incidence of the diseases by governorate, season, age and sex. Composite risk-index scores were estimated to rank the 27 Egyptian governorates into 3 groups: high, medium and low risk. The 15 diseases with the highest incidence were food and waterborne diseases (5 diseases), vaccine-preventable diseases (7 diseases) and others, e.g. hepatitis C infection. Bloody diarrhoea and typhoid had the high incidence for 2006-2013. There were 11 high-risk governorates; Ismailia had the highest risk-index score. The findings suggest the need for specific interventions related to environmental sanitation and improving the childhood immunization programme, particularly in the high-risk governorates.