In this paper we present a cutting plane algorithm for the Set Covering problem. Cutting planes are generated by a “general” (i.e. not based on the “template paradigm”) separation algorithm based on the following idea: i) identify a suitably small subproblem defined by a subset of the constraints of the formulation; ii) run an exact separation algorithm over the subproblem to produce a violated cutting plane, if any exists. Computational results on difficult small-medium size instances are reported.