Box-Behnken Design is a useful tool for the optimization of the chromatographic analysis. The goal of this study was to select the most significant factors that influenced the following parameters of the chromatographic separation: retention time, relative retention time, symmetry of the peaks, tailing factor, a number of theoretical plates, Foley - Dorsey parameter, resolution factor, peak width at half height. The results underwent the ANOVA test to find the statistically significant variables and interactions between them. The level of significance was for p < 0.05. The polynomial equations described quantitatively the statistically significant parameters and the interactions between them. The statistical analysis indicated both the best conditions for the separation of the compounds and the variables that were most influential for peaks' parameters. The four-factor analysis performed for LEVO and MOXI indicated that ACN, TEA and pH are the most significant factors that influence the separation. The analysis for the pair CIPRO and LEVO required six factors. The statistical analysis proved that the most significant factors are ACN, MeOH and TEA. In the separation of these two compounds on the HPLC column, the interaction ACN × MeOH was also significant.