There is considerable interest in developing functional protein arrays on the nanoscale for high-throughput protein-based array technology, and for the study of biomolecular and cell interactions at the physical scale of the biomolecules. To these ends, self-assembly based techniques may be desirable for the nanopatterning of proteins on large sample areas without the use of lithography equipment. We present a fast, general approach for patterning proteins (and potentially other biomolecules) on the nanoscale, which takes advantage of the ability of block copolymers to self-assemble into ordered surface nanopatterns with defined chemical heterogeneity. We demonstrate nanoarrays of immunoglobulin and bovine serum albumin on polystyrene-block-poly(methyl methacrylate) templates, and illustrate the applicability of our technique through immunoassays and DNA sensing performed on the protein nanoarrays. Furthermore, we show that the pattern formation mechanism is a nanoscale effect originating from a combination of fluid flow forces and geometric restrictions templated by an underlying nanopattern with a difference in protein adsorption behavior on adjacent, chemically distinct surfaces. This understanding may provide a framework for extending the patterning approach to other proteins and material systems.