Extruded flat aluminium tubes with multi-parallel ports microchannel heat exchangers are popularly used in automotive air-condition systems. The automotive air-condition is one of the earliest systems that is being banned for using a working fluid with a GWP value higher than 150. HFO-1234yf is one of the most possible candidates to replace the current refrigerant HFC-134a used in it but very few studies have been conducted for flow boiling of HFO-1234yf in rectangular microchannels. This study provides an experimental investigation and comparison on the flow boiling heat transfer of refrigerants HFO-1234yf and HFC-134a in a microchannel heat exchanger with a channel size of 0.5 mm. The test results show that the heat transfer coefficients of HFC-134a are from 0 to 22% higher than those of HFO-1234yf depending on mass velocity and vapor quality. Kandlikar and Balasubramanian (2004) correlation provides the best predictions for the present test results. The major controlling properties for flow boiling heat transfer coefficients in rectangular microchannels is similar to those for flow in larger circular tubes. They are strongly depending on the two-phase flow pattern at various flow conditions.