Human mast cells are a rich and unique source of heparin, which is stored in cytoplasmic secretory granules and accounts for metachromasia, a staining property used to identify mast cells by light microscopy. The sub-cellular locations of heparin in secretory human mast cells and human mast cells recovering from secretion are not known. Acquisition of this knowledge requires ultrastructural imaging of well-preserved cells with a visible probe which binds to heparin. We sought to develop this knowledge regarding human mast cell secretion by using a labelling method for heparin that depends on the well-known property of ribonuclease inhibition by heparin. Human lung mast cells were isolated, partially purified, either stimulated or not stimulated to secrete with anti-IgE, and recovered 20 min or 6 h later for routine electron microscopy. Histamine secretion was also determined. A previously developed post-embedding, enzyme-affinity-gold electron microscopic technique to image ribonucleic acid (RNA) with ribonuclease-gold (R-G), which also binds to the enzyme inhibitor, heparin, was employed to determine the sub-cellular locations of heparin in non-secretory and secretory mast cells as well as in mast cells recovered from short-term cultures after secretion. Specificity controls for the novel use of this method and quantification of granule labelling in these controls were performed. Heparin was labelled by R-G in electron-dense granules within non-secretory human lung mast cells (HLMCs), in electron-dense granules that persisted in secretory HLMCs at the maximum histamine secretion time (20 min), and in electron-dense granules within recovering HLMCs. Specificity controls showed that gold alone did not label HLMCs and that absorption with heparin significantly reduced or abrogated HLMC granule staining with R-G, but that RNA absorption did not. Heparin stores were absent in newly formed, electron-lucent intracytoplasmic degranulation channels in secretory HLMCs. Electron-dense granule matrices in the process of extrusion to the cell exterior still retained heparin at the instant of cellular secretion. Non-granule heparin stores bound R-G in recovering HLMCs. These locations included resolving degranulation channels, as newly emergent granules partitioned and condensed within them, and electron-dense content-containing vesicles and progranules within synthetic mast cells. Ultimately, all known ultrastructural patterns of HLMC granules developed in recovering cells, and each of them contained heparin. Heparin was secreted from HLMCs which were stimulated by anti-IgE, and heparin was recovered by a combination of conservative and synthetic mechanisms in HLMCs after a secretory event.