Antibody microarray based technology is a powerful emerging tool in proteomics, target discovery, and differential analysis. Here, we report the first study where recombinant antibody fragments have been used to construct large scale antibody microarrays, composed of 127 different antibodies against mostly immunoregulatory antigens. The arrays were based on single framework recombinant antibody fragments (SinFabs) designed for high on-chip stability and functionality, and were used for the analysis of malignant and normal stomach tissue samples from Helicobacter pylori positive and negative patients. Our results demonstrate that distinct tumor as well as infection associated protein expression signatures could be identified from these complex tissue proteomes, as well as biomarkers such as IL-9, IL-11 and MCP-4, previously not found in these diseases. In a longer perspective, this study may improve the understanding of H. pylori induced stomach cancer and lead to development of improved diagnostics.