Capillary electrophoresis (CE) coupled with laser-induced fluorescence (LIF) is a powerful method for the trace analysis of cellular components. This review presents a summary of topics for the direct analysis of anthracyclines and multidrug resistance proteins in cancerous cells. A micellar electrokinetic chromatography (MEKC) method that does not use organic solvents, and hence prevents the precipitation of proteins in cellular samples, was shown to be a reliable method for the determination of several anthracyclines including the epimeric doxorubicin and epirubicin. A fast CE-based immunoassay for investigating transporter multidrug resistance associated protein (MRP1) was also developed for routine or explorative analysis of the levels of transporter proteins in cancerous cells. A combination of the developed MEKC-LIF method and the CE immunoassay (CEIA) method has permitted the analysis of anthracyclines and MRP1 in a cell line to show the relationship between the levels of MRP1 and amount of anthracyclines in cancerous cells.