An external quality assessment (EQA) program for molecular detection of avian influenza A (H7N9) virus was implemented by National Center for Clinical Laboratory (NCCL) of China during June 2013. Virus-like particles (VLPs) that containing full length RNA sequences of hemagglutinin (HA), neuraminidase (NA), matrix protein (MP) and nucleoprotein (NP) genes from the H7N9 virus (armored RNAs) were constructed. The EQA panel comprising 6 samples with different concentrations of armored RNAs positive for H7N9 viruses and four H7N9-negative samples (including one sample positive only for MP gene of the H7N9 virus) was distributed to 79 laboratories in China that carry out molecular diagnosis of H7N9 viruses. The overall performances of data sets were classified according to the results of both H7 and N9. Consequently, 80 data sets were received (one participant provided two sets of results), which were generated using commercial (n = 60) or in-house (n = 17) real-time RT-PCR (qRT-PCR) kits and commercial assay employed isothermal amplification method (n =3). The results revealed that the majority (82.5%) of data sets correctly identified "H7N9 virus" while 17.5% of the data sets need to improve their diagnostic capability. The "improvable" data sets were derived mostly from false-negative results of N9 at relatively low concentrations. The false-negative rate was 5.6% and the false-positive rate was 0.6%. In addition, we observed varied diagnostic capabilities between different commercially available kits and in-house developed assays, with assay manufactured by BioPerfectus Technologies (Jiangsu, China) performing better than others did. Overall, the majority of laboratories have reliable diagnostic capacity.