Micro-injection moulding is becoming increasingly important among the available processes for production of micro-electromechanical systems (MEMS) and microsystem technologies (MSTs), and higher number of polymer products is being manufactured by this process. Due to the sensitive nature of applications of this process, such as medical and aerospace applications, achieving high quality parts with high dimensional accuracy is crucial. In this work, a design of experiment (DoE) approach is used. The aim is to study the effects of three process parameters which are commonly used for research in this domain, on the dimensional accuracy of microchannels with different sizes; they are injection velocity, injection pressure, and melt temperature. The study focuses on two polymers, polyoxymethylene (POM) and liquid crystal polymer (LCP). Experimental results showed that higher melt temperature and injection pressure resulted in higher dimensional accuracy. Nevertheless, high settings for the three parameters resulted in higher percentage of flash in most cases. In conclusion, the most influential factors were shown to be melt temperature and injection pressure.