Finite element analysis was performed to analyze structural safety of a new heavy-duty direct injection diesel engine. A half section of the in-line 6-cylinder engine was selected as a computational domain. A mapping method was used to project heat transfer coefficients from CFD results of engine coolant flow onto the FE model. The accurate setting of thermal boundary condition on the FE model was expected to result in improved prediction of temperature, cylinder bore distortion, and stresses. Characteristics of high cycle fatigue were investigated by assuming the engine was operated under the following five loading conditions repeatedly; assembly force, assembly force with thermal loading, alternating maximum gas pressure loading at each cylinder combined with assembly force and thermal loading. Distribution of fatigue safety factor was calculated by using it Haigh diagram in which the maximum and the minimum stresses were selected from the five loading cases.