Trioctylphosphine oxide capped cadmium selenide quantum dots, synthesized in organic media were rendered water soluble by silica overcoating. Silanisation was done by a simple reverse microemulsion method using aminopropyl silane as the silica precursor. Further, the strong photoluminescence of the silica-coated CdSe quantum dots has been utilized to visualize rabbit adipose tissue-derived mesenchymal stem cells (RADMSCs) and Daltons lymphoma ascites (DLA) cancerous cells in vitro. Subsequently the in vivo fluorescence behaviours of QDs in the tissues were also demonstrated by intravenous administration of the QDs in Swiss albino mice. The fluorescence microscopic images in the stem cells, cancer cells and semi-thin sections of mice organs proved the strong luminescence property of silica-coated quantum dots under biological systems. These results establish silica-coated CdSe QDs as extremely useful tools for molecular imaging and cell tracking to study the cell division and metastasis of cancer and other diseases.