A new procedure using chlorazol black E has been developed for staining vesicular–arbuscular mycorrhizal fungi in cleared roots. In a comparative study, chlorazol black E was found to be much superior to previously used stains (acid fuchsin, trypan blue, aniline blue) for showing details of internal hyphae and particularly arbuscules. This clearing and staining procedure, combined with Nomarski interference contrast microscopy, revealed details of arbuscule structure not evident with previous techniques. Field-collected samples were also stained well by this procedure. The procedure should allow more accurate assessment of roots for colonization by vesicular–arbuscular mycorrhizal fungi.