Lectins are a structurally diverse class of (glyco)proteins which bind mono- and oligosaccharides with high specificity and in a reversible way. For many years, the unique sugar binding properties of plant lectins have been exploited for the development of biochemical tools for glycoprotein isolation and characterisation, and the use of lectins as a glycoprofiling tool has became much more sophisticated with the advent of lectin microarrays, in which a panel of lectins are immobilized on a single chip for glycomic analysis. Among the numerous lectins studied so far, those from legumes represent the largest family. They can be present at relatively high amounts depending on genetic as well as environmental factors, and are accumulated especially in the seeds. For this reason, some lectins as the phytohemagglutinin from the common bean Phaseolus vulgaris constitute a possible risk, since consumption of raw or incorrectly processed beans has been shown to cause outbreaks of gastroenteritis, nausea and diarrhoea. On the other hand, for these anti-nutritional properties, bean extracts enriched in lectins or in lectin-related amylase inhibitors are also finding a growing use as active ingredients of “weight-blockers” in dietetic preparations for obesity treatment. Current methods to determine the lectin levels in foods are based on immunoenzymatic or toxicity tests, which are largely aspecific. Very recently, the availability of proteomic methodologies has allowed to start development and validation of sensitive and specific assays for detecting trace amounts of harmful lectins in either raw or processed foods. In this review, the main aspects of current and perspective applications of mass spectrometry and proteomic technologies to the structural characterisation of legumes are presented, with focus on issues related to detection, identification, and quantification of phytohemagglutinins relevant for their biochemical, immunological and toxicological aspects.