Rapid and reliable methods are fundamental for the comprehensive characterization of emerging and evolving avian influenza viruses. Although microarrays provide new possibilities with their parallel approach, their use in diagnostic laboratories is still limited due to economical and practical factors. An easy-to-use, low-cost microarray-based assay for haemagglutinin subtyping and pathotyping of avian influenza viruses and specific detection of highly pathogenic H5N1/Asia clade 2.2 is described as a novel diagnostic tool. The ArrayTube platform is user-friendly, inexpensive and allows processing of many samples. The sensitivity of the assay developed was comparable to real-time RT-PCR, and the simultaneous detection of different subtypes was possible. Validation with 90 influenza A virus isolates representing all 16 haemagglutinin subtypes and 44 field samples (cloacal swabs from wild and domestic birds) demonstrated the feasibility of the system for sensitive and specific characterization of AIV. Facilitating haemagglutinin subtyping and pathotyping for the majority of influenza A-positive cloacal swabs within 24h, the new assay enables detailed AIV diagnosis even in less well-equipped laboratories.