OBJECTIVE To determine the magnitude and outcome of influenza in southern part of Bangladesh and also to identify intrusion of novel influenza virus. METHODS This study was conducted for two years (2008-2009) in outpatient and inpatient department of both paediatrics and medicine discipline of Khulna Medical College Hospital. Nasal and throat swab specimens were collected from each influenza like illness (ILI) case and kept together in a virus transport media and transported to international centre for diarrhoeal disease and research, Bangladesh laboratory. Influenza virus was detected by rRT-PCR including types and subtypes. RESULTS A total of 526 patients were enrolled during the study period with the mean (SD) age of 19 (17) years. Identification of influenza virus was 14% and positive cases were mostly found in under-five children (24%). The vast majority (88%) of influenza cases were found during April to September. Virus detection rate was higher in inpatient department (IPD) (21%) than in outpatient department (12%). The dominant virus type and subtype was influenza A (87%) and H3 (49%), respectively. Type A was significantly higher than type B in causing severe illness compared to ILI (OR=7.04, 95%CI: 2.76-18.7, P<0.01). Headache and chest indrawing was found in significantly higher proportion (P<0.05) in influenza positive IPD cases. Among 31 hospitalized cases majority (77%) recovered completely except two cases that needed referral for additional support. CONCLUSIONS Influenza mostly affected under-five children and young adult. The peak season here was late summer and rainy season.