Primary immunodeficiency (PID) is a large group of rare diseases present with chronic, serious, or life-threatening infections and other immune complications caused by defects or dysfunction of human immune system. Unlike secondary immunodeficiency acquired from an environmental factor or other medical conditions, PIDs are initiated by genetic defects. PIDs are divided into innate/ adaptive immunodeficiencies, phagocytic deficiencies, complement deficiencies, and immune dysregulation. Due to the heterogeneous nature of the clinical presentations, diagnosis of PIDs can be of significant challenge. Review of clinical history and physical examination is important for raising initial suspicion of PIDs, whereas laboratory testing is essential to establish a diagnosis. Laboratory investigation includes the assessment of antibody and cellular response, as well as evaluation of the phagocytic and complement system. Flow cytometry and genetic assays are generally served as confirmation tools to validate a diagnosis. The recent exponential increase of genetic analysis has facilitated the identification of known and novel mutations. The advances in understanding of the immune system, development of novel cellular and molecular methodologies, and increased clinical awareness have led to significant improvement of disease management and clinical outcome for these diseases.