When the degree of closure of the paper machine wet end waters increases, wet end problems also become more difficult to control without specific and selective on-line measurements. The need to measure the concentrations of individual compounds in order to explain wet end phenomena is growing. This study was performed to set up a CE system to a paper machine and to determine soluble inorganic and organic ions in different locations of pulp and paper process waters with real time analyses by two on-line CE methods. A reconstructed commercial CE apparatus was connected to a papermaking machine via an apparatus, which was a combined sampling and sample pretreatment instrument, the role of which was to filter and dilute the samples before on-line determination by CE. The on-line procedures were optimized for simultaneous determination of anions as chloride, sulfate, oxalate, formate and acetate and for determination of cations as potassium, calcium, sodium, magnesium and traces of aluminium. The quantification was performed with external standard methods using the programs available in the commercial CE instrument. The concentrations of the ions were transferred by using a computerized transfer algorithm exporting the results from the analysis instrument to the process control unit. The developed on-line procedures were tested three times in paper and paperboard mills for 1 month at a time. Correlations were observed between the CE results and changes in the processes.