The use of ultra-high flow-rate chromatography coupled to mass spectrometry offers great potential for the rapid, on-line analysis of pharmaceutical compounds in plasma as it permits high throughput direct analysis of plasma samples without any time-consuming sample preparation such as solid-phase extraction. The coupling of mass spectrometry with high-performance liquid chromatography often results in enhanced selectivity and sensitivity compared to, for example, ultraviolet absorbance detection. This can remove the need for complete resolution of the analyte from endogenous materials in the matrix. The use of large particle size stationary phases, and therefore, the ability to use large porosity column end frits, coupled with the added selectivity and sensitivity of the mass spectrometer allows an on-line analysis approach to be used for the direct analysis of pharmaceuticals in biological matrices with extremely high throughput. This paper presents an overview of the manner in which we have optimised this technique for the analysis of plasma samples, in terms of gradient profile, system configuration and optimal injection volume for maximum throughput and robustness. The nature of the mobile phase flow is also discussed.