This paper presents the study and simulation of two Fuel Cell based Distributed Generation (FCDG) systems. Each of these systems consists of a validated PEM fuel cell model, a DC-DC Boost converter circuit and a 3-phase SPWM inverter circuit. The main difference between the two FCDG systems exists in the DC-DC converter circuit; the first circuit is a DC-DC Boost converter with a 1-phase 3-winding high frequency transformer and the second circuit is the conventional DC-DC Boost converter. The two FCDG systems have been studied under balanced and unbalanced load connection and disconnection. The simulation analysis has been done using MATLAB/SIMULINK platform.