Second Harmonic Generation (SHG) from BiFeO3 nanocrystals is investigated for the first time to determine their potential as biomarkers for multiphoton imaging. Nanocrystals are produced by an auto-combustion method with 2-amino-2-hydroxymethyl-propane-1,3-diol as a fuel. Stable colloidal suspensions with mean particle diameters in the range 100–120 nm are then obtained after wet-milling and sonication steps. SHG properties are determined using two complementary experimental techniques, Hyper Rayleigh Scattering and nonlinear polarization microscopy. BiFeO3 shows a very high second harmonic efficiency with an averaged 〈d〉 coefficient of 79 ± 12 pm/V. From the nonlinear polarization response of individual nanocrystals, relative values of the independent dij coefficients are also determined and compared with recent theoretical and experimental studies. Additionally, the particles show a moderate magnetic response, which is attributed to γ-Fe2O3 impurities. A combination of high nonlinear optical efficiency and magnetic response within the same particle is of great interest for future bio-imaging and diagnostic applications.