Mycotoxins deoxynivalenol (DON) and patulin (PAT) are toxic fungal metabolites that contaminate food commodities worldwide. They pose health risks for humans and animals, and have a negative impact on the economy. Mycotoxin detection is vital to ensure public safety. Although traditional detection techniques for mycotoxin detection (e.g. LC-MS) have proven to be highly selective and sensitive, simpler, more rapid, and more cost-effective approaches are required. Aptamer-based techniques are a possible solution. Aptamers are oligonucleotides that can bind to molecules with high affinity and specificity, generated via an in vitro process known as SELEX. We attempted to generate aptamers for DON and PAT. The selection process for DON was challenging and it would be beneficial to continue SELEX, whereas the process for PAT was simpler thus sequences for potential aptamers were obtained. This work has contributed to the production of aptamer-based assays and biosensors for mycotoxin detection.