In this study a new approach to determine three different siderophores (ferrichrome, ferrichrysin, ferricrocin) in natural soil solutions as well as in cultures of fungi is presented. The method includes enrichment of the analytes on a short pre-column, packed with C18 material, and subsequent highly selective separation of the analytes on a capillary porous graphitic carbon (PGC) column. In contrast to normal C18 packing materials, porous graphitic carbon offers chromatographic resolution between the three very similar analytes. The selectivity of the method is enhanced even further by the electrospray ionization (ESI) mass spectrometric detection. The combination of a short pre-column and a packed capillary separation column results in a method with high sensitivity. Reported detection limits, defined as the concentration giving the signal-to-noise ratio 3:1, is 27.7 pM for ferrichrome, 46.1 pM for ferricrocin and 37.4 pM for ferrichrysin.