This paper considers nonlinearly mixed integer tolerance allocation problems in which both tolerance and process selection are to be decided simultaneously so as to minimize the manufacturing cost. The tolerance allocation problem has been studied in the literature for decades, usually using mathematical programming or heuristic/metaheuristic optimization approaches. The difficulties encountered for both methodologies are the number of constraints and the difficulty of satisfying the constraints. A penalty-guided artificial immune algorithm is presented for solving such mixed integer tolerance allocation problems. Numerical examples indicate that the proposed artificial immune algorithms perform well for the tolerance allocation problem considered in this paper. In particular, as reported, solutions obtained by artificial immune algorithm are as well as or better than the previously best-known solutions.