Abstract The article presents a continuation of research carried out to determine the effect of input parameters (changes in engine structure parameters) on selected output parameters (diagnostic measures), based on quickly changing exhaust gas temperature. A method of determining the simultaneous influence of two input factors (the structure parameter and the engine load) on one output factor was presented, as well as an evaluation of which of the analysed input factors has a stronger influence on the output parameter. The article presents the stages of the experimental research conducted and statistical inference based on the results. Three changing parameters for the structure were reviewed: the active cross-sectional area of the inlet air channel, the injector opening pressure and the compression ratio. Based on the quickly changing temperatures of the exhaust gases, three diagnostic measures were defined and subjected to statistical tests. The following data were averaged over one cycle for a 4-stroke engine operation: the intensity of changes, the specific enthalpy and the peak-to-peak value of the exhaust gas temperature. The results of the two-factor analysis are presented. Conclusions on the analysis are given and a criterion for the selection of a diagnostic measure, depending on the analysed parameter of the structural design of the diesel engine, is proposed. The previous part of the article presented the results of the first stage of the elimination study: the one-factor statistical analysis (randomised complete plan). This paper presents the results of the second stage of the studies: two-factor analysis (block randomised plan), where the significance of the effect of changing the values of the structural parameters on the diagnostic measures were analysed in the background of a variable engine load. The next (third) part will present the results of the calculations and analysis of the interaction coefficient of significance.