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. The design of experiments method was used to investigate the composition-process – properties relationship. Results indicated that the process variables significantly affected the flow patterns and resulting morphology during the filling stage of the microinjection molding (lIM) process, using 0.45 mm diameter lIM samples. Two distinct flow regimes have been identified in lIM using the low cross-section samples. The first was a conventional “fountain flow,” which resulted in a skin/core structure and reduced volume resistivity up to 10 X cm in the case of 5% CNTs and up to 100 X cm in 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 was a “plug flow” due to wall slippage, obtained under low injection speeds, low mold temperatures, and low rotation velocities, leading to a substantial increase in modulus of elasticity (60%) with increased electrical resistivity up to 103 X cm for 5% CNTs and 105 X cm 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. It was concluded that in lIM, the process conditions should be closely monitored. In the case of high viscous heating, degradation of mechanical properties was obtained, while skin- core morphology formation enhanced electrical conductivity.