The SNaPshot technique, also known as minisequencing, is a primer extension-based method developed for the analysis of Single Nucleotide Polymorphisms (SNPs). Using this technique, it is possible to analyze more than 50 SNPs distributed throughout the genome in a single multiplex reaction, making it an advantage when compared with traditional sequencing reaction. In this chapter, you will find a step-by-step guide to design a multiplex primer assay for SNaPshot reaction.