Secondary metabolites are chemical compounds that are not directly involved in the normal growth, development or reproduction of organisms. Due to the toxicity shown by some of these compounds, their presence can represent a threat to human health. Reliable detection systems able to control their presence are required, as a tool to ensure public health. This chapter offers an overview of different techniques developed for the detection of toxic secondary metabolites, taking ochratoxin A and microcystins as two representative examples. While ochratoxin A is a mycotoxin produced by several species of fungi, microcystins are cyanotoxins released by certain strains of cyanobacteria. Biosensor-based strategies are emphasized as powerful screening tools.