Wet apple core rot (wACR) is a well-known disease of susceptible apple cultivars such as Gloster, Jona Gold, and Fuji. Investigations in apple orchards in Slovenia identified Fusarium avenaceum, a known producer of several mycotoxins, as the predominant causal agent of this disease. A LC-MS/MS method was developed for the simultaneous detection of thirteen F. avenaceum metabolites including moniliformin, acuminatopyrone, chrysogine, chlamydosporol, antibiotic Y, 2-amino-14,16-dimethyloctadecan-3-ol (2-AOD-3-ol), aurofusarin, and enniatins A, A1, B, B1, B2, and B3 from artificially and naturally infected apples. Levels of moniliformin, antibiotic Y, aurofusarin, and enniatins A, A1, B, and B1 were quantitatively examined in artificially inoculated and naturally infected apples, whereas the remaining metabolites were qualitatively detected. Metabolite production was examined in artificially inoculated apples after 3, 7, 14, and 21 days of incubation. Most metabolites were detected after 3 or 7 days and reached significantly high levels within 14 or 21 days. The highest levels of moniliformin, antibiotic Y, aurofusarin, and the combined sum of enniatins A, A1, B, and B1 were 7.3, 5.7, 152, and 12.7 microg g(-1), respectively. Seventeen of twenty naturally infected apples with wACR symptoms contained one or more of the metabolites. Fourteen of these apples contained moniliformin, antibiotic Y, aurofusarin, and enniatins in levels up to 2.9, 51, 167, and 3.9 microg g(-1), respectively. Acuminatopyrone, chrysogine, chlamydosporol, and 2-AOD-3-ol were detected in 4, 11, 4, and 10 apples, respectively. During wet apple core rot, F. avenaceum produced high amounts of mycotoxins, which may pose a risk for consumers of apple or processed apple products.