Owing to their usual conditions of production in countries with warm and humid climates and to poor storage conditions, products derived from Capsicum sp. are susceptible to fungal contamination and development, which can lead to the accumulation of mycotoxins in these foods. Thus, products as chilli or paprika can be contaminated with fungal toxins, such as aflatoxins, ochratoxins and other mycotoxins, which pose a serious risk to public health. This study reviews the main aspects regarding mycotoxin contamination of Capsicum, in the context of the importance of this product in a global market and approaches the effect of processing on final contamination of foods, as well as reviews the analytical methodology commonly employed in fungal and mycotoxin analysis in these types of products.