Seven Delta-disaccharide standards from heparan sulfate/heparin (HS/H) and nine Delta-disaccharide standards from chondroitin/dermatan sulfate (CS/DS) and hyaluronic acid (HA) were derivatized with the fluorophore 2-aminoacridone (AMAC) and separated in two runs each by reversed-phase HPLC with baseline separation and very short run times. This novel method facilitates the separation of the largest number of Delta-disaccharides from both CS/DS/HA and HS/H with one column and buffer system after fluorophore labeling in two runs at present. For the first time nine glycosaminoglycan (GAG) Delta-disaccharides from CS/DS/HA were separated after fluorophore labeling in one run. The limits of quantification (LOQs) were below 0.2 pmol for CS/DS/HA and HS/H Delta-disaccharides. We demonstrated applicability of our method for biological samples. Furthermore, normal ranges of the GAG Delta-disaccharide compositions from platelets and granulocytes were determined for the first time.