Two-phase flow in micro scale heat exchangers is considered a promising cooling technique for electronic and other high heat flux devices. Different operating conditions and heat exchanger geometries can lead to different flow patterns, pressure drop and heat transfer characteristics. The performance of two different designs was examined in this study, namely: a microgap and a micro multi-channel configuration. Both heat sinks were manufactured from oxygen-free copper using a high precision micro-milling machine. The microgap was 1 mm high, 20 mm wide and 25 mm long, i.e. had a base area of 20 × 25 mm², with the fluid entering and exiting vertically in the inlet and outlet plenum. The micro multi-channel heat sink had the same base area, with 40 channels, 0.7 mm high, 0.35 mm wide separated by a wall 0.15 mm thick, with the fluid entering and exiting vertically in the plena. The base heat flux ranged from 34 to 440 kW/m², while the mass flux varied from 100 to 200 kg/m² s. The inlet sub-cooling was kept low, at 5 K for both heat sinks. The experiments were performed at atmospheric system pressure. The working fluid used was HFE-7100, a dielectric and eco-friendly refrigerant. Flow visualization was carried out using a high-speed, high-resolution camera. The flow patterns, heat transfer coefficient and pressure drop for the two geometries were obtained and compared. The performance index, i.e. the ratio of the heat transfer rate to the total pressure drop, was also calculated and compared for the two examined geometries.