Real-time PCR (qPCR) methods are adequate tools for sensitive and rapid detection and quantification of toxigenic molds contaminating food commodities. Methods of qPCR for quantifying zearalenone (ZEA)-, sterigmatocystin (ST)-, cyclopiazonic acid (CPA)-, and patulin (PAT)-producing molds have been designed on the basis of specific target genes involved in the biosynthesis of these mycotoxins. In this chapter reliable qPCR protocols to detect and quantify such toxigenic molds are described. All of these methods are suitable when working with mold pure cultures and mold contaminated foods. For ZEA-producing molds, two qPCR using the SYBR Green fluorochrome and based on two polyketide synthase (PKS) genes are detailed. qPCR protocols relied on the fluG and the idh genes able to quantify ST- and PAT-producing molds, respectively, which can be performed by both SYBR Green and TaqMan methodologies are described. Regarding CPA-producing molds a TaqManq PCR method including a competitive internal amplification control is detailed. Since DNA extraction is a critical step in the detection and quantification of toxigenic molds by qPCR, a protocol for extracting DNA from mold pure cultures and food is also described.