Capillary electrophoresis methods are reported for the determination of trace levels of substances possibly present as contaminants on equipment used in pharmaceutical manufacturing. A previously reported method for the determination of a range of basic drugs was optimised through use of internal standards and a shorter length capillary. This method was used to establish an optimised extraction procedure through analysis of solutions containing a range of drugs with different solubilities. A CE method for the trace level analysis of a range of different acidic drugs was shown to be capable of achieving acceptable precision and sensitivity. Levels of detergent solution residue were monitored by quantifying potassium levels using indirect UV detection. These methods are in routine use within our laboratories.