This article reports the development of highly waterborne silicon quantum dots (Si QDs) terminated with a reactive group for grafting of biomolecules. Hydrogen-terminated QDs were prepared by thermal disproportionation of amorphous hydrogen silsesquioxane derived from triethoxysilane followed by hydrofluoric etching. Next, the hydrogenated Si surfaces were exposed to 10-undecenoic acid at different temperatures in Ar atmosphere, yielding the termination of the QDs with a carboxyl group. The thermal hydrosilylation of 10-undecenoic acid yielded the termination of the QDs with a carboxyl group. An increase in molecular coverage of an undecanoic acid (UA) monolayer resulted in both the enhanced increase of zeta-potential in a negative direction for a greater water-dispersity and the increase of absolute quantum yield (QY) of photoluminescence (PL). PLQY improved for ~ 1% to 26% with increasing UA coverage. We assessed the molecular interaction between the UA-SiQDs and HeLa cells by means of cellular uptake experiments using the QDs with different UA coverages. Results showed that the QDs with the highest dispersity in water were not internalized in the cells under confocal fluorescence microscopic observation. In contrast, the QDs with lower coverage of UA monolayer were internalized by endocytosis when incubated with HeLa cells. This contrasting observation opens the possibility of successfully preparing carboxy-capped SiQDs that do not allow cellular uptake but are targeted to specific cells by appropriate conjugation with biomolecules.