A sequential fractionation procedure based on (i) water extraction, (ii) hexane extraction, (iii) saccharification, and (iv) proteolysis was developed to provide the first ever data on the molecular distribution of iron in maize. This was completed by the operational determination of the iron bioavailability using an in-vitro simulated model for gastro-intestinal digestion. The coupling of hydrophilic interaction chromatography (HILIC) and size exclusion chromatography (SEC) with the parallel detection by inductively coupled plasma mass spectrometry (ICP-MS) and high resolution electrospray mass spectrometry (HR-ESI-MS) allowed the identification of water-soluble Fe(III)-mugineate, Fe(III)-(citrate)2, and Fe(III)2-(phytate)2. The procedures were applied to study some well characterized maize varieties having shown previously differences in iron bioavailability during cell culture and animal model feeding studies. The combined analytical methods developed in this work could unambiguously discriminate low from high Fe bioavailable seeds in these closely related maize varieties.