Factor analysis (FA) was performed for some analgesic, anti-inflammatory and antipyretic drugs to model relationships between molecular descriptors and HPLC retention parameters. FA performed using 26 sets of structural parameters, 26 sets of HPLC retention data, and considering all parameters together (52 parameters) led to the extraction of two main factors. The first principal component (factor 1) accounted for 65-73% of the variance in the data. The second principal component (factor 2) explained 27-35% of data variance. Moreover, of the 52 parameters tested, the highest influence on factor value was found with chromatographic parameters and selected structural parameters (i.e., energy quantum-chemical parameters and electron affinity specifying parameters). Additionally, the pattern of distribution of individual drugs within the plane determined by the two principal components (factors 1 and 2) was in good agreement with their pharmacological (analgesic, anti-inflammatory and antipyretic) properties. The findings are discussed from the point of view of structure-activity relationships.