Microfluidics and lab-on-a-chip technology offers unique advantages for the next generation devices for diagnostic therapeutic applications. For chemical, biological and biomedical analysis in microfluidic systems, there are some fundamental operations such as separation, focusing, filtering, concentration, trapping, detection, sorting, counting, washing, lysis of bio-particles, and PCR-like reactions. The combination of these operations led to the complete analysis systems for specific applications. Manipulation of the bio-particles is the key ingredient for these applications. Therefore, microfluidic bio-particle manipulation has attracted a significant attention from the academic community. Considering the size of the bio-particles and the throughput of the practical applications, manipulation of the bio-particles is a challenging problem. Different techniques are available for the manipulation of bio-particles in microfluidic systems. In this review, some of the techniques for the manipulation of bio-particles; namely hydrodynamic based, electrokinetic-based, acoustic-based, magnetic-based and optical-based methods have been discussed. The comparison of different techniques and the recent applications regarding the microfluidic bio-particle manipulation for different biotechnology applications are presented. Finally, challenges and the future research directions for microfluidic bio-particle manipulation are addressed. © 2014 Elsevier B.V.