There is burgeoning interest in protein microarrays, but a source of thousands of non-redundant, purified proteins was not previously available. Here we show a glass chip containing 2,413 non-redundant purified human fusion proteins on a polymer surface, where densities up to 1600 proteins/cm2 on a microscope slide can be realised. In addition, the polymer coating of the glass slide enables screening of protein interactions under non-denaturing conditions. Such screenings require only two hundred microlitres sample volumes, illustrating their potential for high-throughput applications. Here we demonstrate two applications, (i) the characterization of antibody binding, specificity and cross-reactivity and (ii) profiling the antibody repertoire in body fluids, such as serum from patients with auto-immune diseases. For (i), we have incubated these protein chips with anti-RGSHis6, anti-GAPDH, and anti-HSP90b antibodies. In an initial proof of principle study for (ii), we have screened serum from alopecia and arthritis patients. With analysis of large sample numbers, identification of disease-associated proteins to generate novel diagnostic markers may be possible.