The objective of this study was to evaluate the occurrence of alternariol (AOH) and alternariol monomethyl ether (AME) in commercial foods as well as their resistance to food processing techniques. A survey was conducted on the presence of Alternaria mycotoxins in 116 apple and tomato products purchased from Canadian markets in the Spring of 2016. AOH and AME were found in 50% and 30% of these products respectively. The highest concentrations found were 75 μg/kg for AOH and 30 μg/kg for AME. In a second experiment tomato juice spiked with 80, 200, and 500 μg/kg of AOH and AME was subjected to high temperature and high pressure processing. A treatment of 121°C for 20 min reduced AOH content by 13.2% and AME by 15.3%. Processing at 600 MPa for 5 min reduced AOH by 24.9% and 12.8%.