1. A method for adaptive runtime reconfiguration of a co-processor instruction set, in a computer system with at least a main processor communicatively connected to at least one reconfigurable co-processor, wherein the co-processor has been configured to implement an instruction set comprising one or more co-processor instructions, the method comprising the steps of: issuing a co-processor instruction to the co-processor; determining whether the instruction is mapped to the co-processor; for an instruction not mapped to the co-processor instruction set, evaluating the need for reconfiguring the co-processor based on performance; reconfiguring the instruction set of the co-processor when the evaluation indicates said reconfiguration is needed; and executing the instruction.