A comparative investigation was performed on the effects of hydroxypropyl-beta-cyclodextrin (HP-beta-CD) on the growth, biocatalytic activity, and cell integrity of Arthrobacter simplex TCCC 11037 (ASP) and Mycobacterium sp. NRRL B-3683 (MSP). The addition of HP-beta-CD to ASP medium improved its cell wall permeability for lipophilic compounds but significantly inhibited its growth and biocatalytic activity. On the other hand, the addition of HP-beta-CD to MSP broth had lesser effects. Atomic force microscopy scanning analysis revealed that HP-beta-CD damaged the cell integrity in ASP, especially the outermost cell surface structure, but not in MSP, which remained intact, owing to the differences in their cell wall and cell membrane composition. Protein leaking and lipid content in ASP increased with increased HP-beta-CD concentration, indicating possible alterations in ASP cell membrane features caused by HP-beta-CD. These alterations may also explain the slow cell growth and decreased cell Delta Im in ASP upon the addition of HP-beta-CD.