Geochemical, petrophysical, and depth to the Paleozoic-Precambrian basement interface from drill hole data for Mesoproterozoic igneous rocks and iron ore deposits of the St. Francois Mountains, southeast Missouri (MMDB) are provided in this data release. The samples were collected as part of various agency programs and projects from 1967 through 2019. Most samples were collected by agency personnel and analyzed in agency laboratories, under contracts in commercial analytical laboratories, or in the field. The geochemical data compilations include historical geochemical data archived in the USGS National Geochemical Database (NGDB), the Missouri Geological Survey (MGS) of the Missouri Department of Natural Resources, and other sources. The data tables describe historical and new quantitative and qualitative geochemical analyses. The analytical results were determined by 120 laboratory and field analytical methods performed on 8,250 rock and 25 mineral samples. The MMDB data are the most accurate and complete to date and should be useful for a wide variety of geochemical studies. The petrophysical data set contains measurements of density and magnetic susceptibility of Mesoproterozoic igneous rocks in southeast Missouri. Density and magnetic susceptibility measurements are also made on drill core and hand samples collected at the iron-oxide apatite (IOA) and iron-oxide copper gold (IOCG) deposits at Pea Ridge (IOA), Iron Mountain (IOA), Pilot Knob (IOA), Shepard Mountain (IOA), and Cedar Hill (IOA), Bourbon (IOA) and Boss (IOCG). In addition, measurements of samples from outcrops and drill cores were made on unmineralized regional geologic units across the St. Francois terrane. The drill hole depth and stratigraphic data from 2,681 drill holes that penetrated the Paleozoic-Precambrian unconformity are also included in this database.