Traditional epidemiological investigation of nosocomial transmission of influenza involves the identification of patients who have the same influenza virus type and who have overlapped in time and place. This method may miss-identify transmission where it has not occurred or miss transmission when it has. We applied influenza virus whole genome sequencing (WGS) to an outbreak of influenza A in a haematology/oncology ward and identified two separate introductions; one which resulted in 5 additional infections and 79 bed-days lost. Results from WGS are becoming rapidly available and may supplement traditional infection control procedures in the investigation and management of nosocomial outbreaks.