The non-coding regions (NCRs) of influenza A virus gene segments play a crucial role in the viral replication cycle. Although the NCRs are considered to be conserved, some variation does exist, that affects viral replication. Therefore, a rapid method to sequence the 5´ and 3´ NCRs was designed. This method is based on ligation of viral RNA, RT reactions and subsequent PCR with primersets consisting of a gene segment specific primer and a primer designed across the junction of the 5´ and 3´ ends. These PCR fragments can be sequenced directly without the need for cloning PCR fragments first. This method was used to sequence the NCRs of A/Bilthoven/16190/68 (H3N2) and A/Turkey/Turkey/1/05 (H5N1).