A new approach is presented to solve the problem of a long separation time in the second dimension of comprehensive two-dimensional chromatography. The need for a rapid separation in the second column is overcome by repeating analysis of a sample many times. In each of these individual analysis cases the sample is injected into the first dimension column and after a delay a low amount of the effluent at the end of the first column is sampled to the second-dimensional column. The time interval between the samplings from the first column to the second column is constantly increased. Thus, the system enables a comprehensive analysis of the effluent emerging from the first into the second column. This approach, which we call stroboscopic sampling, is tested for coupling high-performance liquid chromatography (HPLC) to capillary electrophoresis (CE) by an interface which operates on the principle of transporting the effluent from the HPLC column to the capillary inlet by small pressure pulses (0.5 MPa). The performance of the interface for accomplishing the comprehensive HPLC-CE analysis was demonstrated for an on-line connection of a short ion-exchange column and an ion-exclusion column to the CE capillary.