Multifunctional nanoparticles based on magnetite/silica core-shell, consisting of iron oxides coated with silica matrix doped with fluorescent components such as organic dyes (fluorescein isothiocyanate - FITC, Rhodamine 6G) or quantum dots, have drawn remarkable attention in the last years. Due to the bi-functionality of these types of nanoparticles (simultaneously having magnetic and fluorescent properties), they are successfully used in highly efficient human stem cell labeling, magnetic carrier for photodynamic therapy, drug delivery, hyperthermia and other biomedical applications. Another application of core-shell-based nanoparticles, in which the silica is functionalized with aminosilanes, is for immobilization and separation of various biological entities such as proteins, antibodies, enzymes etc. as well as in environmental applications, as adsorbents for heavy metal ions. In vitro tests on human cancerous cells, such as A549 (human lung carcinoma), breast, human cervical cancer, THP-1 (human acute monocytic leukaemia) etc. , were conducted to assess the potential cytotoxic effects that may occur upon contact of nanoparticles with cancerous tissue. Results show that core-shell nanoparticles doped with cytostatics (cisplatin, doxorubicin, etc.), are easily adsorbed by affected tissue and in some cases lead to an inhibition of cell proliferation and induce cell death by apoptosis. The goal of this review is to summarize the advances in the field of core-shell materials, particularly those based on magnetite/silica with applicability in medicine and environmental protection. This paper briefly describes synthesis methods of silica-coated magnetite nanoparticles (Stöber method and microemulsion), the method of encapsulating functional groups based on aminosilanes in silica shell, as well as applications in medicine of these types of simple or modified nanoparticles for cancer therapy, MRI, biomarker immobilization, drug delivery, biocatalysis etc., and in environmental applications (removal of heavy metal ions and catalysis).