© 2015 Elsevier Ltd. All rights reserved. It is well established that the contamination of produce destined for human consumption by pathogenic microbes and/or toxins poses a considerable risk to public health and has serious economic consequences. Hence, it is imperative that such analytes are detected through the implementation of rapid, reproducible, and sensitive detection strategies. In this chapter, we provide a critical assessment of three methodologies that incorporate antibody-, enzyme-, or nucleic acid-based probes as biorecognition elements and discuss how these can be applied for high throughput screening of pathogens and toxins in complex food sample matrices.