High-resolution melting (HRM) analysis is a simple, sensitive, and cost-effective screening method. HRM enables the detection of homozygous or heterozygous point sequence variants and small deletions within specific PCR products by observing temperature and shape changes in melting curve profiles using fluorescent dyes. Herein, an updated protocol for routine variant screening of nuclear genes encoding assembly factors and structural subunits of cytochrome c oxidase (COX) is described. Nonetheless, the general recommendations given for HRM analysis can be applicable for examining any genetic region of interest.