Due to its ability to produce low-cost and high repeatable micro polymeric parts, injection moulding of micro components is emerging as one of the most promising enabling technologies for the manufacturing of polymeric micro-parts in in many different fields, from IT to Healthcare, to Medicine. However, when approaching the micro-scale, different issues related to the process should be addressed, especially as the depth of the mould cavity becomes very thin. In particular, the mould roughness could affect the surface quality of the produced micro components, like in macro moulding, as well as the complete filling of the parts. Although micro-injection moulding process has been extensively studied, further research on the effect of mould roughness conditions and on non-Newtonian fluid flow in micro-cavities are required. This will shed a light and open up new paths for a deeper understanding of the moulding scenario. The main objective of the present paper is the evaluation of the influence of the mould roughness on the polymer flow during micro injection moulding process. The test parts have been realized in POM material and have thickness lower than 250 μm. The test part design has been properly conceived in order to neglect the effect of dimensions and geometry and to highlight the roughness contribution during the filling phase of micro injection moulding process. The experimentation has been performed considering cavities with different roughness values (3 levels) and decreasing depths (3 levels), for a total of nine test parts manufactured by micro-electrical discharge machining process (μ-EDM). The results of the experiments are discussed in the paper and show that cavity surface roughness affects the injection process as the moulding scale level is decreased. In particular, when the cavity depths are reduced, higher surface roughness promotes the filling of components and this finding could be ascribed to the increase of wall slip effect.