This work was focused on investigating the effects of two separation influencing parameters in CZE, namely temperature and organic additive concentration upon the electrophoretic migration properties of model tripeptides. Two variable semi-empirical (TVSE) models and back-propagation artificial neural networks (ANN) were applied to predict the electrophoretic mobilities of the tripeptides with non-polar, polar, positively charged, negatively charged and aromatic R group characteristics. Previously published work on the subject did not account for the effect of temperature and buffer organic modifier concentration on peptide mobility, in spite of the fact that both were considered to be influential factors in peptide analysis. In this work, a substantial data set was generated consisting of actual electrophoretic mobilities of the model tripeptides in 30 mM phosphate buffer at pH 7.5, at 20, 25, 30, 35 and 40 C and at four different organic additive containing running buffers (0, 5, 10 and 15% MeOH) applying two electric field strengths (12 and 16 kV) to assess our mobility predicting models. Based on the Arrhenius plots of natural logarithm of mobility versus reciprocal absolute temperature of the various experimental setups, the corresponding activation energy values were derived and evaluated. Calculated mobilities by TVSE and back-propagation ANN models were compared with each other and to the experimental data, respectively. Neural network approaches were able to model the complex impact of both temperature and organic additive concentrations and resulted in considerably higher predictive power over the TVSE models, justifying that the effect of these two factors should not be neglected.