The frequency of some major mycotoxins in marker tissues (liver and kidney) and in muscle tissue of slaughter pigs and cattle, obtained from registered abattoirs in South Africa, was studied. Samples of each three bovine carcasses were obtained from two abattoirs, and samples of three porcine carcasses were from a third abattoir. All samples originated from animals from subsistence farming. All samples were analysed for aflatoxins (AFB1, AFB2, AFG1, AFG2, deoxynivalenol (DON), ochratoxin A (OTA) and zearalenone (ZEN) using immunoaffinity chromatography extract cleanup and high-performance liquid chromatography (HPLC). At a limit of quantification (LOQ) of 1 μg/kg (individual AFs, 100 μg/kg (DON), 1 μg/kg (OTA) and 20 μg/kg (ZEN)), no mycotoxins were detected in any of the samples.