In this paper, we discuss how a holographic interference technique can be applied in the experimental determination of the phase centers of non-standard horn antennas in the millimeter-waveband. The phase center is the point inside the horn from which the radiation appears to emanate when viewed from the far-field, and knowing its location is necessary for optimizing coupling efficiencies to quasi-optical systems. For non-standard horn designs, and other feed structures, the phase center may be difficult to reliably predict by simulation, in which case, before committing to antenna manufacture, there is a requirement for it to be determined experimentally. Although the phase center can be recovered by direct phase measurement of the far-field beam pattern, this usually involves expensive instrumentation such as a vector network analyzer for millimeter wave horn antennas. In this paper, we describe one inexpensive alternative, which is based on measuring the interference pattern in intensity between the radiation from the horn of interest and a reference beam derived from the same coherent source in an off-axis holography setup. The accuracy of the approach is improved by comparison with the interference pattern of a well-understood standard horn (such as a corrugated conical horn) in the same experimental setup. We present an example of the technique applied to a profiled smooth-walled horn antenna, which has been especially designed for cosmic microwave background (CMB) polarization experiments.