A new formulation for tracking multiple particles in slow viscous flow for microfluidic applications is presented. The method employs the manipulation of the boundary element matrices so that finally a system of equations is obtained relating the rigid body velocities of the particle to the forces applied on the particle. The formulation is specially designed for particle trajectory tracking and involves successive matrix multiplications for which SMP (Symmetric multiprocessing) parallelisation is applied. It is observed that present formulation offers an efficient numerical model to be used for particle tracking and can easily be extended for multiphysics simulations in which several physics involved. Copyright © 2015 Tech Science Press.