The use of microcontroller boards are extremely common in day to day lives, to such an extent that it is impossible to live without them. The choice of controllers is numerous. In the market today, with rich features for every board it is hard to choose the best one. This research paper aims to compare two microcontroller boards and to point out pros and cons of both boards. The two controllers chosen are Intel Atom board SeYS9400 powered by Intel Atom processor E6xx series and Intel Galileo Board powered by quark X1000 processor. The application chosen is automotive/robotic application. Comparing all the features of each board and juxtaposing each with the other a conclusion is drawn regarding the best one for automotive embedded system application. Keywords-compon Galileo board; Intel atom board; microcontroller board.