The use of a single set of microemulsion electrokinetic chromatography (MEEKC) separation conditions has been assessed for its applicability in the analysis of a range of pharmaceutical compounds. Particular emphasis was placed on neutral or very hydrophobic compounds, which can be difficult to analyse by conventional capillary electrophoresis. The microemulsion employed for the majority of separations consisted of 0.81% w/w octane, 6.61% w/w 1-butanol, 3.31% w/w sodium dodecyl sulphate and 89.27% w/w 10 mM sodium tetraborate buffer. Good separations of methyl, ethyl, butyl and propyl hydroxybenzoates, and a range of ionic and neutral water soluble and insoluble compounds was achieved using a single set of separation conditions. A number of novel applications of MEEKC were developed included the simultaneous determination of the active components and preservatives in liquid formulation and determination of drug related impurities. Improved performance was obtained through use of internal standards and preparation of the samples dissolved in the microemulsion solution. Validation aspects such as linearity, repeatability, accuracy, injection precision and sensitivity were successfully assessed.