Holo-chaperonin from Thermus thermophilus (Thermus holo-cpn) is a bullet-shaped particle where chaperonin-10 heptamer locates at one axial end of the cylindrical body of chaperonin-60 tetradecamer. Thermus holo-cpn promotes in-vitro folding of denatured 3-isopropylmalate dehydrogenase (IPMDH) from the same bacterium. We observed the complexes of Thermus holo-cpn and folding intermediates of IPMDH by immuno-electron microscopy after decoration by single layer labeling with anti-IPMDH IgG or by double layer labeling with anti-IPMDH IgG as first layer and antibodies against IgG as second layer. Images of the electron microscope showed that anti-IPMDH IgG was bound to the bottom end of the bullet-shaped Thermus holo-cpn. This result provides direct evidence that the folding intermediate binds to the axial end, which is opposite to the end where chaperonin-10 heptamer resides, of the cylindrical body of chaperonin-60 tetradecamer, and that bound folding intermediate in the complex is sufficiently exposed to the outside to be accessible by antibody.