The effect of particle shape on its transport and retention in porous media was evaluated by stretching carboxylate-modified fluorescent polystyrene spheres into rod shapes with aspect ratios of 2:1 and 4:1. Quartz crystal microbalance with dissipation (QCM-D) experiments were conducted to measure the deposition rates of spherical and rod-shaped nanoparticles to the collector (poly-l-lysine coated silica sensor) surface under favorable conditions. The spherical particles displayed a significantly higher deposition rate compared with that of the rod-shaped particles. Theoretical analysis based on Smoluchowski-Levich approximation indicated that the rod-shaped particles largely counterbalance the attractive energies due to higher hydrodynamic forces and torques experienced during their transport and rotation. Under unfavorable conditions, the retention of nanoparticles in a microfluidic flow cell packed with glass beads was studied with the use of laser scanning cytometry (LSC). Significantly more attachment was observed for rod-shaped particles than spherical particles, and the attachment rate of the rod-shaped particles showed an increasing trend with the increase in injection volume. Rod-shaped particles were found to be less sensitive to the surface charge heterogeneity change than spherical particles. Increased attachment rate of rod-shaped particles was attributed to surface heterogeneity and possibly enhanced hydrophobicity during the stretching process.