We studied the conformation and physical properties of cyclic and linear isomaltooligosaccharides in aqueous solution by intrinsic viscosity measurement, small angle X-ray scattering (SAXS) and molecular modeling. We used four cycloisomaltooligosaccharide samples (CIs) with degree of polymerization (DP) 7–10 (CI-7–CI-10) and five linear isomaltooligosaccharide samples (LIs) with DP 7–11 (LI-7–LI-11). The values of α in the Mark–Houwink–Sakurada equation [η]=KMwα for the CI and LI were determined to be 0.50 and 0.78, respectively. The radii of gyration (RG) of CI-7, CI-8, CI-9 and CI-10 determined from SAXS data were 6.7, 6.9, 7.5 and 8.3Å, respectively. The scattering profile of CI-9 compared with those obtained for molecular models indicated that CI molecular chains are less flexible than those for LIs and adopt a rather compact circular conformation.