We review the current status of the use of focused electron beam induced deposition (FEBID) for the growth of magnetic nanostructures. This technique relies on the local dissociation of a precursor gas by means of an electron beam. The most promising results have been obtained using the Co₂(CO)₈ precursor, where the Co content in the grown nanodeposited material can be tailored up to more than 95%. Functional behaviour of these Co nanodeposits has been observed in applications such as arrays of magnetic dots for information storage and catalytic growth, magnetic tips for scanning probe microscopes, nano-Hall sensors for bead detection, nano-actuated magnetomechanical systems and nanowires for domain-wall manipulation. The review also covers interesting results observed in Fe-based and alloyed nanodeposits. Advantages and disadvantages of FEBID for the growth of magnetic nanostructures are discussed in the article as well as possible future directions in this field.