Natural dyestuffs used for painting or dyeing of textiles are complex mixtures of compounds of various chemical properties. Proper identification of the dye used by a painter and, even better, its origin is possible only when its compositional 'fingerprint' can be evaluated. For this reason gradient program for liquid chromatographic separation of 16 color compounds--components of natural blue dyes: elderberry, logwood and indigo--has been developed. Two detector systems were used simultaneously: UV-Vis spectrophotometry (at 280, 445, 520 and 600 nm) and ESI mass spectrometry (positive and negative SIM mode). It was found that fragmentation observed in ESI-MS is affected not only by ion source parameters, but also by chromatographic conditions, especially in case of the less stable substances: cyanidin glucosides, tannic acid, rutin and hematoxylin. Examination of characteristic dissociation pathways of the compounds under investigation after direct admission into ion source or after chromatographic separation allowed to select proper ions for SIM detection and to develop novel and efficient reversed phase high performance liquid chromatographic (RP-HPLC)-UV-Vis/ESI-MS method for the analysis of natural blue dyes. The procedure was successfully applied for identification of indigotin and carminic acid-main colorants extracted from a fiber taken from the blue-red 'Italian' tapestry (the collection of the National Museum in Warsaw, Poland).