The technical development of automated Sanger sequencing in the 2000s followed by next-generation sequencing (NGS) in the 2010s, has enabled significant advancements in the molecular diagnosis of inherited diseases. The launch of France’s first National Rare Diseases Plan in 2011 further supported the establishment of rare disease centers and networks of rare diseases. Concurrently, NGS platform were integrated into molecular biology laboratories, enabling the first diagnoses using Targeted Exome Sequencing (TES) (gene panel). These approaches have been progressively implemented at very high throughput, evolving from Whole Exome Sequencing (WES, which analyzes all coding regions of the human genome) to Whole Genome Sequencing (WGS), the latter being integrated into the France Genomic Medicine 2025 plan initiated in 2016. In this review, we compare TES, WES, and WGS, and discuss their respective advantages, limitations, and future prospects, as well as their applications in the field of endocrinology.