Mycotoxins are toxic secondary metabolites produced by some filamentous fungi from Aspergillus, Fusarium, Penicillium, Alternaria and Claviceps genera. These metabolites are stable chemical compounds and persist during processing and heat treatment, so they can contaminate food and animal feed causing a broad spectrum of adverse effects both in humans and animals. In addition, mycotoxins can bioaccumulate in organs, and tissues, thereby affecting the nervous, endocrine, and immune systems; or can be excreted by biological fluids or faeces, being able to use as biomarkers of mycotoxin exposure. The most common are aflatoxins (B1, B2, G1, and G2), ochratoxin A, fumonisins, trichothecenes, zearalenone and patulin, although approximately 400 different mycotoxins have been described to date. Moreover, unaltered mycotoxins are not the only source of exposure since, as part of their defence against xenobiotics, plant and living organisms may alter their chemical structure. Liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) is commonly used for determining mycotoxins. However, not all mycotoxins or modified mycotoxins are commercially available as reference standards for use in monitoring, and, as a result, interest in high resolution mass spectrometry (HRMS) is increasing. More specifically, Orbitrap and time-of-flight (TOF) mass analysers have emerged as the most useful technique for mycotoxin determination. HRMS has important advantages over other methods, including the ability to record full scan spectra by measuring the accurate mass of analytes, the screening of untargeted compounds, a high degree of structural confirmation, and retrospective analysis data that offer the possibility of investigating analytes that were not considered at the time of spectral acquisition. This review discusses recent studies for the targeted and untargeted determination of mycotoxins in urine, blood and other relevant biological samples using strategies based on HRMS.