The thermal performances of Fuel Cells depend on the temperature distribution inside them. The operating temperature of the Fuel Cell is an important parameter that influences extremely the lifetime of the system. Proton Electrolyte Membrane Fuel Cells (PEMFC) have been considered for transport applications because they operate at low temperatures, between 80°C and 100°C. In order to carry out the uniformity of the temperature and the dissipated heat flux, the two phase flow cooling system is required for this application. Boiling in minichannels is used in the compact heat exchanger for many interesting applications such as: the transport industry, electronics, chemical industry, etc. We are conducted an experimental study for convective boiling inside a minichannels which have the hydraulic diameter of 800µm. The test section is a compact heat exchanger consisting of a set of fifty parallel, rectangular minichannels machined on the top of a copper block. Some thermocouples are placed inside the wall in order to measure the temperatures. The inverse heat conduction problem is solved to evaluate the thermal boundary conditions: the surface temperature, the heat flux and the local heat transfer coefficient. The Iterative Regularization Method is used to solve the inverse problem. Experiments are conducted by varying the electrical heat flux used for visualizing the different flow patterns inside the parallel minichannels. The power dissipated and the fluid flow are variable.