The mechanical, electrical, thermal and rheological properties of micro injection molded nanocomposites comprising 2% and 5% carbon nanotubes (CNTs) incorporated in polycarbonate (PC) and polyamide 66 (PA) were studied. Design of experiments method was used to investigate the process - properties relationship. Results indicated that the process variables had a significant effect on the flow patterns and resulting morphology during the filling stage of the micro injection molding (MIM) process, using a 0.45 mm diameter MIM samples. Two distinct flow regimes have been identified in MIM using the low cross-section samples. The first, is a conventional "fountain flow", which resulted in a skin/core structure and reduced volume resistivity up to 10 Ωcm in the case of 5% CNTs and up to 100 Ωcm in the case of 2% CNTs, in both polymers, respectively. In addition, inferior mechanical properties were obtained, attributed to polymer degradation under high shear rate conditions, when practicing high injection speeds, high mold temperatures and high screw rotation velocities. The second is a "plug flow", due to wall slippage, obtained under low injection speeds, low mold temperatures and low rotation velocities, leading to substantial increase in modulus of elasticity (60%) with increased electrical resistivity up to 103 Ωcm for 5% CNTs and 105 Ωcm for 2% CNTs, respectively. The rheological percolation threshold was obtained at 2% CNTs while the electrical threshold was attained at 0.4% CNTs, in both polymers. The process conditions affected both the glass transition temperature of PC and the degree of crystallinity of the PA. It was concluded that in MIM, the process conditions should be closely monitored. In the case of high viscous heating degradation of mechanical properties has been obtained, while in the case of skin core/low morphology formation enhanced electrical conductivity has been achieved.