In this paper we propose a flow based on the Bayesian Optimization Algorithm (BOA) for mapping pipelined applications on a heterogeneous multiprocessor platform on Field Programmable Gate Array (FPGA) with customizable processors. BOA is a Probabilistic Model Building Genetic Algorithm (PMBGA) that, substituting the classical mutation and crossover operators with the construction and the sampling of a Bayesian network, is able to identify correlated sub-structures within the problem to be maintained while generating new solutions. The paper introduces the model adopted for pipelined applications and then shows why BOA fits the problem better than other search algorithms, like Genetic Algorithm (GA), Simulated Annealing (SA) and Tabu Sear...