The ability to quantify ultra-low concentrations of biologically active compounds in biological matrices is essential for the study of pharmacological/toxicological effects occurring at low doses. Selective solid-phase extraction (SPE) was combined with highly sensitive capillary LC (microLC)-MS/MS analysis to achieve ultra-sensitive quantification of the anti-cancer drug paclitaxel in cancer cells. The optimized SPE selectively extracted paclitaxel and eliminated undesirable matrix compounds, thus enabling a high sample loading volume on the microLC column without compromising chromatographic performance and operational robustness. The validated lower limit of quantification (LOQ) was 5pg/mL, approx. 20-fold more sensitive than published LC-MS/MS methods. The calibration curve was linear over the range of 5-6250pg/mL. Accuracy was 98-109% and the variation (CV%) was 2.3-7.4%. This method was applied successfully to quantify temporal drug accumulation by A121a ovarian cancer cells treated with sub-ng/mL concentrations of paclitaxel.