While designing the layout of any manufacturing organizations, the primary objective is to decide an optimal arrangement of their departments (machines or cells) in a two-dimensional shop floor (facility) satisfying desired objectives, which is termed facility layout problem (FLP). In traditional layout design philosophy, the inter-cell layout and flow path layout design of material handling system (MHS) was carried out step by step in a sequential manner. This results in sub-optimal solutions for FLP. In this paper, an integrated approach is adopted to design the inter-cell layout and the flow path layout of MHS simultaneously. The quality of the final layout is evaluated by minimizing the weighted sum of two distance-based cost objectives namely, (1) total material handling cost. (2) Distance-weighted cost of total closeness rating score. Sequence-pair (SP) representation is used for layout encoding. The translation from SP to layout is efficiently done by longest common subsequence methodology. Due to NP-hard nature of the proposed problem, an elitist strategy genetic algorithm (ESGA) is developed and tested with three test problem instances available in the literature. It is found that the proposed ESGA algorithm is able to produce the best solutions consistently, twice faster than the standard GA for the test problem instances. © 2012 Springer-Verlag London Limited.