MicroRNAs (miRNAs) are potential biomarkers in the diagnosis of human disease. In this study, a novel concept, the miRNA network biomarker, was proposed for the selection of biomarkers. Each miRNA network biomarker contains miRNA targets, as well as Transcription Factors (TFs), that affect the miRNA expression. The obtained biomarkers were applied to classifying expression data sets in different progression stages from chronic gastritis to gastric cancer. Furthermore, these biomarkers could accurately (94%) discriminate gastric cancer samples from normal samples in another data set. Angiogenesis-related pathways and genes were found to be enriched in these network biomarkers.