This paper describes the experimental setup for waste heat recovery system and power generation using thermo electric devises (TEDs) for a water -cooled diesel engine with carbon neutral fuel such as biodiesel fuel. This paper reports the system integration of heat exchanger of engine systems, power conditioning using MPPT control and DC-DC converter by power conversion circuit through battery charging operation. As a result, a value of an open circuit voltage for evaluating at maximum output of TEDs should be modified from that at non-generation condition to that at power generation condition due to the reduction of the difference of temperature between surfaces of TEDs at power generation because of occurrence of Peltier effect as output current from TEDs increases. Furthermore, the circuit performance was evaluated, then it was shown that the power utilization efficiency is around 98 %, and the power conversion efficiency is around 91 %, then these values are almost the same as those previously evaluated by simulated power source.