We have probed one antiferromagnetic (AF) antiphase boundary (APB) and a single Fe(3)O(4) domain using nanogap contacts. Our experiments directly demonstrate that, in the case of probing one AF-APB, a large magnetoresistance (MR), high resistivity, and a high saturation field are observed as compared with the case of probing a single Fe(3)O(4) domain. The shape of the temperature-dependent MR curves is also found to differ between the single domain and one of the AF-APB measurements, with a characteristic strong temperature dependence for the single domain and temperature independence for the one AF-APB case. We argue that these observations are indicative of profound changes in the electronic transport across APBs. The investigated APB defects increase the activation energy and disturb the long-range charge ordering of monodomain Fe(3)O(4).