Gene mutations are a hallmark of cancer. Although mutations can occur due to various endogenous and extracellular stress factors daily, detecting them is not straightforward. The HPRT gene is one of the housekeeping genes and is essential for the nucleotide salvage pathway. However, it is not strictly necessary since the de novo pathway can compensate for nucleotides synthesis. By using 6-thioguanine, a cytotoxic purine analog, as a selection agent, we can eliminate HPRT-proficient cells and quantify mutation frequency. Moreover, molecular techniques can provide further analysis of these mutations. This chapter introduces the basic method for analyzing HPRT mutation frequency in Chinese hamster ovary (CHO) cells and highlights potential pitfalls in the experiments.