Recently, semiconductor nanocrystals or quantum dots (QDs) aroused great concern because of their unique properties such as the size-dependent photoluminescence. They have many excellent applications in areas of molecular bioimaging, medical detection and even energy, especially as biosensing and imaging instead of fluorescent dyes. For the bio-safety, however, we should assess the cytotoxicity of QDs before used in biomedical imaging. Here, the cytotoxicity of amino-functionalized CdSe/CdS (CdSe/CdS-NH2) QDs and carboxy-functionalized CdSe/CdS (CdSe/CdS-COOH) QDs was investigated by MTT assay method. According to our findings, both CdSe/CdS-NH2 and CdSe/CdS-COOH have a dose-dependent effect on cell proliferation. The cytotoxicity of QDs varies with storing time of QDs and kinds of cells. The cytotoxicity of QDs modified with -COOH or -NH2 groups both vary with concentrations in positive linear or change with QD storing time in negative linear. The results indicate that CdSe/CdS-COOH QDs have lower toxicity than CdSe/CdS-NH2 QDs. Hela cell is somewhat more sensitive to amino- and carboxy-modified QDs than Bel7404 cell for MTT assays.