A miniaturised analytical system for separating and detecting a range of steroidal oestrogens, based on the coupling of a micromachined capillary electrophoresis chip with glassy-carbon electrode amperometric detector, is described. Factors influencing the on-chip separation utilising the technique micellar electrokinetic chromatography (MEKC) and detection processes are optimised. The addition of modifiers such as organic solvents and surfactants improve separation and resolution of these hydrophobic compounds. Using a borate running buffer (5 mM, pH 11) with 20% methanol and SDS (20 mM) and a separation voltage of 2000 V, baseline resolution is observed for 16-keto-17β-oestradiol, oestriol, 11β-hydroxyoestradiol, oestrone, and β-oestradiol in 420 s with limits of detection 16–84 μM. The implications for on-site environmental analysis are discussed.