An approach to isolating small aggregates of single-wall carbon nanohorns (SWNHs) is presented. SWNHs are ultrasonically treated in an aqueous solution of surfactant, resulting in dispersion of SWNH aggregates. Subsequent centrifuging enables the separation of small aggregates from larger aggregates or agglomerations and removal of graphitic particles (GG balls), the main impurity. The SWNHs obtained in this way were purified and formed small aggregates, thus exhibiting characteristics superior to those of SWNHs before treatment. We believe that the ability to isolate small SWNH aggregates in an aqueous solution should contribute to their application in the fields of biological sensing and drug delivery systems.