A new capillary electrophoresis (CE) method for monitoring renally excreted varenicline (VAR), highly effective drug prescribed in the case of smoking cessation, in human urine was developed. The method, based on the two-dimensional (column-coupled) CE separation with UV detection, provided advantage of the on-line sample preparation and, by that, sensitivity and selectivity enhancement. The capillary isotachophoresis (cITP) on-line sample treatment included stacking of the sample in a large volume and simple elimination of the major matrix constituents. The second dimension, capillary zone electrophoresis (CZE) with cyclodextrin selector, provided fine baseline separation of the analyte from the rest of sample matrix constituents. The developed method was validated according to the FDA guideline for bioanalytical method validation (limit of detection, lower limit of quantification, linearity, precision, and accuracy). Favorable performance parameters of the proposed method as well as its simplicity, high effectivity, and low cost indicated its potential for the routine biomedical use. It was successfully applied to monitor the changes of VAR concentration levels in human urine samples (Figure 1). The data obtained of the method were consistent and comparable also with data published in literature. This work was supported by the projects VEGA 1/0873/15, KEGA 022UK-4/2015, APVV-15-0585 and carried out in the Toxicological and Antidoping Center at the Faculty of Pharmacy Comenius University in Bratislava.