Two microscale separation techniques for the analysis of bioactive naphthoquinones in Eleutherine americana were developed and validated. By MEKC four compounds (eleuthoside B, isoeleutherin, eleutherol and eleutherinoside A) could be determined in plant extracts using an aqueous electrolyte solution composed of 25 mM sodium tetraborate, 50 mM sodium cholate and 20% THF. CEC on a polymeric methacrylate-based monolith with strong cationic properties showed promising results, as it additionally enabled the separation of two enantiomers, eleutherin and isoeleutherin. The mobile phase for CEC experiments comprised 3 mM ammonium formate in a mixture of ACN and water. At an applied voltage of -25 kV, all five markers were baseline separated in less than 12 min. Both methods were successfully validated for linearity (MEKC: R(2) > or = 0.999; CEC: R(2) > or = 0.997), sensitivity (MEKC: LOD = 4-5 microg/mL; CEC: LOD=2-8 microg/mL), accuracy (MEKC: 96.5-102.7% recovery; CEC: 97.1-103.5% recovery) and precision (MEKC: sigma(rel) < or = 2.43%; CEC: sigma(rel) < or = 2.21%). The quantitative analysis of naphthoquinone derivatives in several E. americana samples showed that both methods are suitable for practical applications, because the results were well comparable to those obtained by established techniques such as HPLC.