The creation of microfluidic chips with reagents embedded in the reaction chamber can significantly simplify preparatory procedures and reduce the time when analyzing a sample using RT-PCR. The work examines and discusses some of the key processes that occur during RT-PCR analysis in microfluidic polycarbonate chips with lyophilized reagents. An assessment of the deformation of a polymer chip due to thermal expansion under cyclic temperature changes in the range of 60–95 °C indicates the need to take these effects into account when designing chips from thermoplastic materials. A preliminary calculation of the sample loading conditions shows that maintaining the temperature in the range from 50 to 90 °C for 5 min before starting the analysis ensures an almost uniform distribution of primers throughout the reaction chamber due to diffusion movement and additional measures to intensify this process are not required.