Fe-doped synthetic geomimetic chrysotile nanocrystals represent a reference standard to investigate the health hazard associated with asbestos fibers and constitute interesting inorganic nanotubes for specific technological applications in light harvesting systems, optoelectronics and photonics. As the fiber toxicity is catalyzed by iron ions in specific crystallographic sites and the mechanical behaviour of synthetic chrysotile nanotubes is strongly affected by the iron doping extent, the characterization of Fe substitution to Mg and/or Si sites in the chrysotile structure appears highly important. By EPR, DRS spectroscopic analyses and magnetic investigations, Mg and/or Si ion replacement by Fe(3+) in a synthetic geomimetic chrysotile structure has been investigated. The results highlight that, as a function of the Fe doping extent and of the Fe doping process, iron can replace both Mg and Si sites. The contemporary iron substitution into the octahedral and tetrahedral sheets is associated with the presence of both of isolated Fe(3+) centres in high-spin 3d(5) configuration (S = 5/2, (6)A(1)((6)S)) in O(h) and T(d) symmetry and of intra-lattice clustered species. Increasing the Fe doping extent increases the concentration of aggregated species, while magnetic susceptibility confirms a paramagnetic anisotropy. The results allow to define the opportunity of using or not metallic Fe during the synthesis to obtain doped chrysotile nanocrystals with tailored morphological and structural properties suitable as a reference to study asbestos toxicity and apt to prepare new inorganic nanotubes and quantum wires for innovative technological applications.