This paper presents an efficient continuous real-time routing strategy, namely threshold-based alternate routing (TAR), to minimize mean flowtime of parts in a FMS with routing flexibility. TAR routes parts to alternate machines instead of their primary machines when the benefit in terms of waiting time obtained from routing to an alternate machine exceeds a pre-determined threshold value. This study proposes that the threshold value for each manufacturing system is unique and presents a methodology for determining its unique value. The threshold concept and the performance of TAR in minimizing mean flowtime are tested with extensive experimentation, involving intricate experimental design. TAR provides very significant improvements in system performance measures compared to other real-time rerouting methods and shows that the threshold value is unique and dependent on system parameters for each manufacturing system. The relationship between the threshold value and system parameters has also been determined. (c) 2004 Elsevier B.V. All rights reserved.