Background: Influenza is an acute respiratory disease that continues to cause global epidemics and pandemics in human with significant mortality and morbidity. Objectives: This study was designed to identify the circulating influenza virus in Ibadan, Nigeria during the 2006/2007 season. Methods: Throat swab samples were collected from patients presenting with acute respiratory tract infection at the Out-Patient Departments of major hospitals in Ibadan over a period of seven months from November 2006 to May 2007. Isolation of influenza virus was performed using Madin-Darby Canine Kidney cell line and 10 days old chicken embryonated egg. Isolates was identified by haemagglutination and haemagglutination-inhibition assays using selected CDC Influenza reference antisera (A, B, subtype H1 and H3). Results: Out of 128 patients tested, 21(16.4%) yielded positive for virus isolation. Identification of the isolates showed that 19(14.8%) were positive for influenza virus out of which 11(8.6%) and 8(6.2%) were influenza A and B viruses respectively. Influenza A virus 6(4.7%) were subtype H1; 4(3.1%) were co-subtype H1 and H3; and 1(0.8%) was not inhibited by subtype H1 and H3. Conclusion: The circulation of influenza virus A and B in this study is important to contributing knowledge and data to influenza epidemiology and surveillance in Nigeria.