In this work, the effect of temperature in isothermal and programmed modes on several chromatographic parameters such as retention factor, selectivity, resolution and plate number has been discussed. A critical comparison of isocratic/isothermal, gradient/isothermal and isocratic/program temperature modes has been made. Two representative families of pesticides have been selected for this study. One includes ionisable chlorophenoxy acids and two of their esters, some of which show similar polarities. The other one contains several weakly polar carbamates. Analysis was carried out using a reversed-phase capillary high-performance liquid chromatography (HPLC) system and focusing technique with UV or diode array detection (DAD).