The application of a column switching HPLC system to the analysis of the antimalarial proguanil and its two metabolites in plasma and saliva is described. The assay is based on a previously developed hydrophobic ion-pairing separation using sodium dodecylsulphate on ODS Hypersil. The use of a precolumn to concentrate and allow pre-treatment of these drugs in the two matrices is shown. This is followed by the transfer and subsequent separation of the biguanides by the analytical phase containing a high concentration of hydrophobic pairing ion. It is found that such on-line sample pre-treatment can yield comparable analytical characteristics to off-line solid phase extraction procedures if the precolumn is conditioned between sample injections. The columns can be used for large numbers of saliva assays but when plasma is the biological matrix components of the plasma cause rapid deterioration of the precolumn.