Food products can be contaminated by toxic proteins and peptides derived from many different flources at any stage of the production chain. Food contamination represents a major public health concern, and for this reason, monitoring of food production has become crucial for preventing food poisfining. Proteomic-based methods constitute powerful tools for qualitative and quantitative determination of toxins in both raw ingredients and processed food matrices. This chapter presents an overview of the most common protein and peptide toxins contaminating food and critically describes the advanced proteomic approaches developed for their detection and control.