The field of nanoparticle related research for the diagnosis and therapy of diseases evolves rapidly. Magnetic nanoparticles in combination with magnetizable implant materials for the treatment of implant related infections present a possible implementation in orthopedics. Magnetic nanoporous silica nanoparticles (MNPSNPs) were developed and equipped with fluorescent dyes. In vitro/in vivo biocompatibility and in vivo biodistribution were examined to appraise their potential applicability. Cell culture tests with NIH-3T3 and HepG2 cell lines indicated a good in vitro biocompatibility. Ferritic and titanium alloy (control) plates were implanted subcutaneously at the hind legs of Balb/c mice. Immediately after i.v. or s.c. injection of MNPSNPs, the caudal half of the mice was placed between the poles of an electro magnet. Exposure to the electromagnetic field of approx. 1.7 T was maintained for 10 minutes. 10 animals each were euthanized at days 0, 1, 7, 21 or 42, respectively. Quantity of MNPSNPs in liver, spleen, kidney, lung and skin/muscle samples was assessed by fluorescent microscopic methods. MNPSNP existence on the implant surface was also appraised after several steps of detachment. MNPSNPs showed a time-dependent accumulation in the organs after i.v. injection with initial accumulation in the lungs followed by redistribution to liver and spleen. After s.c. injection no systemic distribution but local appearance of MNPSNPs could be found. First histological evaluation showed no pathological changes after i.v. injection. With good in vivo biocompatibility, future focus will be laid on increasing circle life time of MNPSNPs and evaluation in an infection model.