This Real-Time PCR genotyping protocol can be used for the detection of polymorphisms at codons 146 (N/S/D), 211 (R/Q) and 222 (Q/K) in the caprine PRNP gene. We developed four seperate Real-Time PCR reactions with four different Custom TaqMan® SNP Genotyping Assays (Applied Biosystems, Foster City, California, USA). Each SNP Genotyping Assay consisted of a mix of sequence-specific forward and reverse primers to amplify the polymorphic sequence of interest and two TaqMan® MGB probes, FAM and VIC dye-labeled to detect the amplified product.