This study concerns the technique electric field-assisted capillary liquid chromatography. In this technique, an electric field is applied over the separation capillary in order to provide an additional selectivity. In this technique, the electric field is applied in-line in the separation capillary and here the electric current is the factor limiting the magnitude of applied electric field. The influence of Joule heating and other factors on the current in such systems has been investigated. The temperature in the capillary was first measured within a standard CE set-up, as function of effect per unit of length. Then the same cooling system was applied to an in-line set-up, to replicate the conditions between the two systems, and thus the temperature. Thus Joule heating effects could then be calculated within the in-line system. It was found that for systems applying an electric field in line, the direct influence from Joule heating was only relatively small. The pH in the capillary was measured in the in-line set-up using cresol red/TRIS solutions as pH probe. Significant changes in pH were observed and the results suggested that electrolysis of water is the dominant electrode reaction in the in-line system. In summary, the observed conductivity change in in-line systems was found to be mainly due to the pH change by hydrolysis of water, but primarily not due the temperature change in the capillary column.