This paper describes the construction of a combinatorial artificial receptor array (CARA) and the application of the array to differentiation of proteins based on their binding patterns. Microarrays displaying 5035 unique binding environments were prepared using a library of 19 small molecule building blocks. Each building block was equipped with a carboxylic acid handle, allowing mixtures of the building blocks to be spotted onto the surface of an amine functionalized glass slide for covalent immobilization as subunits of the binding environments. This strategy employs the microarray surface as the receptor synthesis platform, which allows for flexibility in array preparation and agility in application. An advantage of the CARA strategy is the enormous flexibility it enables in the construction of alternate microarray configurations, which facilitates rapid access to the breadth and depth of binding space. Four fluorescently labeled proteins, ubiquitin, myoglobin, alpha-1-acid glycoprotein and lysozyme, were incubated with the arrays to demonstrate the reproducibility of binding and the level of differentiation that can be achieved. The binding environments are stable, scalable, and adaptable to other formats.