Information on the prevalence of influenza, circulating virus subtypes and seasonality is essential for selecting strains for annual vaccines and for planning immunization programmes. Data were obtained from the 13 sentinel surveillance sites throughout Egypt during 2012–2015. Laboratory-confirmed influenza was found in 13% of cases of influenza-like illness (ILI) and 18% of cases of severe acute respiratory infection (SARI); positivity for influenza was similar in cases of ILI and SARI in patients up to 15 years of age but increased for SARI and decreased for ILI in people aged ≥ 15 years. The most commonly observed influenza virus subtypes were B followed by A/H3 in ILI cases, and A/H1N1 followed by B in SARI cases. The seasonality of influenza in ILI cases was November–February, and that in SARI cases was November–March, peaking in January.