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Alternaria is one of the major mycotoxigenic fungal genera with more than 70 reported metabolites. Alternaria mycotoxins showed notably toxicity, such as mutagenicity, carcinogenicity, induction of DNA strand break, sphingolipid metabolism disruption, or inhibition of enzymes activity and photophosphorylation. This review reports on the toxicity, stability, metabolism, current analytical methods, and prevalence of Alternaria mycotoxins in food and feed through the most recent published research. Half of the publications were focused on fruits, vegetables, and derived products—mainly tomato and apples—while cereals and cereal by-products represented 38%. The most studied compounds were alternariol, alternariol methyl ether, tentoxin, and tenuazonic acid, but altenuene, altertoxins (I, II, and III), and macrosporin have been gaining importance in recent years. Solid-liquid extraction (50%) with acetonitrile or ethyl acetate was the most common extraction methodology, followed by QuEChERS and dilution-direct injection (both 14%). High- and ultraperformance liquid chromatography coupled with tandem mass spectrometry was the predominant determination technique (80%). The highest levels of alternariol and alternariol methyl ether were found in lentils, oilseeds, tomatoes, carrots, juices, wines, and cereals. Tenuazonic acid highest levels were detected in cereals followed by beer, while alternariol, alternariol methyl ether, tenuazonic acid, and tentoxin were found in legumes, nuts, and oilseeds.