Magnetic fluids or ferrofluids as they are often called mainly consist of nano sized iron oxide particles ((FeO4)-O-3 or gamma-Fe2O3) that are suspended in carrier liquid. In recent years, substantial progress has been made in developing technologies in the field of magnetic microspheres, magnetic nanospheres and ferrofluids. Techniques based on using of these biocompatible magnetizable complex systems have found application in numerous biological fields viz. diagnostics, drug targeting, molecular biology, cell isolation and purification, radio immuno assay, hyperthermia causing agents for cancer therapy, nucleic acid purification etc. Biocompatible ferrofluids normally use water as a carrier medium. In order to prevent agglomeration the magnetic nanoparticles have to be stabilized by ionic interaction, a bilayer of an appropriate agent (e.g. fatty acid), aspartic and glutamic acid or peptides. Alternatively, the coprecipitation of ferrous/ferric ions is performed in the presence of appropriate biopolymer such as dextran, polyethylen glycol or polyvinyl alcohol. It has been shown that proteins and enzymes can be bound covalently to freshly prepared magnetite in the presence of carbodiimide. Several clinically important enzymes and proteins that include bovine serum albumin, streptokinase, chymotrypsin, dispase, glucose oxidase (GOD) etc., have been immobilized based on this method. The immobilized enzymes showed about 50-80 % of the original added enzyme activity. This contribution will summarize the information about the ways to synthesize biocompatible magnetic nanoparticles and complexes containing them and the application of magnetic complex systems in biomedicine at magnetic drug targeting and hyperthermia.