The substrate material and active side characteristics can affect the bubble ebullition cycle and consequently the heat transfer rate and pressure drop in microchannel evaporators. This paper presents an experimental study on flow boiling patterns, heat transfer rates and pressure drop in multi-microchannels evaporators made of copper and aluminium. HFE-7100 was used as the test fluid at atmospheric pressure, 5 K inlet sub-cooling, mass flux of 50-250 kg/m2s and wall heat flux up to 174 kW/m2. All heat sinks were made with channel width 0.46 mm, channel height 0.46 mm, giving a 0.46 mm channel hydraulic diameter. The heat sink base area was 25 mm in length and 20 mm in width. The experimental results showed that similar flow patterns were visualised for copper and aluminium namely bubbly, slug, churn and annular flow. The heat transfer coefficient in the aluminium heat sink was 12% (average value) higher than that found in the copper heat sink. The measured pressure drop in the aluminium heat sink was 28% (average value) higher compared to the copper heat sink. However, the additional pumping power required to move the fluid through the heat exchanger is small for this factor to be significant. The SEM images of the surface revealed that the number of cavities (possible nucleation sites) was higher in the aluminium surface with clear-cutting marks compared to the copper surface. This may explain the different pressure drop and heat transfer behaviour. The results of the present study indicate that aluminium heat sinks can offer comparable thermal performance to that of copper heat sinks and can also be recommended for cooling high heat flux systems.