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In recent years the analysis of natural products has been carried out using a range of approaches, but mainly utilizing liquid chromatography (LC) or gas chromatography (GC). However, alternative approaches with orthogonal selectivity like capillary electrophoresis (CE) and supercritical fluid chromatography (SFC) have increasingly been employed as well, even though they are often considered niche techniques only. In this study, we intended to confirm and compare their suitability as reliable state-of-the-art methods for the analysis of bioactive compounds by developing CE and SFC for the analysis of dihydrochalcones (DHCs) in apple leaves. The analytes were chosen as they have shown interesting pharmacological effects, such as anti-inflammatory, anti-tumor and immunomodulatory activities, and also present an interesting analytical challenge due to their structural similarity and polarity range. Both methods were well capable to separate the five standard compounds within short separation times and fulfilling the demands for an environmentally friendly "green" technology. CE as well as the SFC assay were validated for linearity, sensitivity, accuracy and precision according to ICH guidelines and met all respective requirements. Using the optimized methods, several Malus sp. samples were analyzed whereby a significant difference in the qualitative as well as quantitative DHC profile was revealed, with overall DHC concentrations ranging from 5.47% to 17.24%. [ABSTRACT FROM AUTHOR]