The paragenesis, textures, and chemical compositions of magnetite in two mafic to intermediate intrusions and four IOA deposits in SE Missouri were studied to discriminate between igneous and hydrothermal sources. In this study, we found that replacement magnetite with mineral inclusion-rich cores yields erroneously high Ti, Al, Si, Mg, and Mn contents as determined by EMP and LA-ICP-MS due to rutile and silicate inclusions. Thus, identification of high-Ti microlites on the basis of inclusion-rich cores with high Ti contents is an analytical artefact. Since the high-Ti magnetite microlite flotation model is critically dependent on this type of analysis, it may be invalid. The presence of coarse-grained high-Ti vein magnetite with ilmenite lamellae enveloped by replacement magnetite with inclusion-rich cores in ore zones suggests that the veins were high-temperature conduits for low-temperature replacement ores. The trace element compositions of vein and replacement magnetite suggest that iron was sourced from mafic to intermediate intrusions. These results support a magmatic-hydrothermal origin for IOA systems in SE Missouri.