Abstract Mesoporous silica nanoparticles (MSNs) with colloidal stability have attracted increasing interest because of their important properties, such as high transparency and cell uptake. Colloidal MSNs are comprehensively reviewed from the viewpoints of their preparation, characterization, and applications which include biomedical, catalytic, and optical materials. The following two points have been emphasized. The first point is that this review covers the widest range of introduction and discussion of the preparation and applications of both colloidal and noncolloidal MSNs. The second point is that this account contains a discussion from the viewpoints of both inorganic and colloid chemistries. After the introduction of the historical background of preparation of MSNs, preparative methods of colloidal MSNs and the major factors for the preparation of nanosized and colloidal MSNs are discussed. The methods to control the size, composition, morphology, and pore size of MSNs are also presented. Appropriate methods to obtain MSNs with high colloidal dispersibility are also discussed. Applications of colloidal MSNs are introduced with an emphasis on the colloidal stability. Issues to be addressed for further developments of colloidal MSNs are finally described.