In this work, we study the effect of elemental iodine as a halide intermediary in the synthesis of FePt3 nanoparticles using a co-reduction of Fe(acac)3 and (NH4)2PtCl2 with 1,2-hexadecanediol. Our study shows that elemental iodine facilitates the formation of FePt3 nanoparticles with the L12 structure. When iodine is not used, the as-made nanoparticles have mostly the disordered fcc FePt3 structure. The as-made nanoparticles are ferromagnetic and have a Curie temperature close to 380 K. Annealing of the as-made nanoparticles leads to an increased particle size and a transformation to the ordered L12 FePt3 phase. Nanoparticles annealed at 700°C for 30 minutes show a mixture of two magnetic phases, a ferromagnetic phase with a lower ordering temperature of ∼300 K and an antiferromagnetic phase with a Néel temperature around 135 K.