Physics-based models of diesel engines with exhaust gas recirculation and a variable geometry turbine (EGR/VGT) have been developed extensively in the control system design community. However, these models omit the heat transfer effects of the charge-air cooler and the recirculated exhaust gas cooler in order to avoid the added complexity in model order for online implementation. Generally, there is no need to include these effects if the purpose of the model is to control the target variables, such as boost pressure and air-to-fuel ratio. In this paper, after surveying the existing state of physics-based models for the EGR/VGT subsystem, a comprehensive model of the EGR/VGT subsystem is developed. This model includes heat transfer effects in the coolers, pressure drops across air filters and pipes, and mass flow rate calculations for a variable geometry turbine and an exhaust gas recirculation control valve. The purpose and scope of this work is offline modeling-for-diagnostics. Such models, though complex, will assist in the fault sensitivity analysis of a subsystem while avoiding any destructive testing when a major design modification in the EGR/VGT subsystem is proposed. For example, the impact of charge-water or EGR cooler degradation on the boost pressure and the air-to-fuel ratio can be studied with such models to further help in designing diagnostic reasoning strategies. Simulation performed using the proposed physics-based model demonstrates a dominant failure effect of an EGR cooler coolant leak over a charge-water cooler water leak on the properties of the intake air.