Primary immunodeficiencies (PIDs) encompass a heterogeneous group of inherited disorders characterized by impaired immune function, leading to increased susceptibility to infections and autoimmune complications. Accurate and timely diagnosis is crucial for implementing appropriate treatment strategies and improving patient outcomes. Genetic and molecular assessments have revolutionized PID diagnosis, moving beyond traditional phenotypic characterization based solely on clinical presentation and immunological laboratory tests. Here we outline the current landscape of genetic and molecular approaches used in PID diagnosis, highlighting their strengths and limitations. Next-generation sequencing (NGS) technologies, including whole-exome sequencing (WES) and whole-genome sequencing (WGS), have significantly advanced PID diagnostics. These powerful techniques allow for simultaneous analysis of numerous genes associated with known PIDs, providing a comprehensive assessment of the patient's genome. WES, focusing on protein-coding regions, offers a cost-effective approach with high diagnostic yield, often identifying causal variants in a substantial proportion of patients with suspected PIDs. WGS, while more expensive, provides a complete picture of the genome, enabling identification of non-coding variants and structural variations that might be missed by WES. Targeted gene panels, focusing on a pre-selected set of genes relevant to specific PID subtypes, offer a faster and more cost-effective alternative for patients with a suspected specific diagnosis. However, challenges remain in interpreting NGS data. The identification of variants of uncertain significance (VUS) is common, requiring further functional studies and family segregation analyses for definitive classification. Furthermore, the genetic heterogeneity of PIDs, with many disorders caused by mutations in multiple genes, can complicate the interpretation of NGS results. Advanced bioinformatic analyses and sophisticated data interpretation pipelines are crucial for effectively navigating this complexity. In addition to NGS, other molecular techniques such as quantitative PCR (qPCR), flow cytometry, and functional assays continue to play important roles in characterizing the specific immunological defects and guiding targeted therapies. In conclusion, genetic and molecular assessments are indispensable for the diagnosis of PIDs, providing significant improvements in diagnostic accuracy and speed compared to traditional methods. While NGS technologies have emerged as powerful tools, careful interpretation of results, coupled with a comprehensive clinical and immunological evaluation, remains essential for accurate diagnosis and effective management of these complex disorders. Future advancements in NGS technologies, bioinformatics, and functional assays will further refine our ability to diagnose and treat PIDs, ultimately improving patient outcomes.