Immune system diseases include both immunodeficiency disorders and autoimmune conditions, where the immune response is either insufficient or inappropriately directed at self-tissues. These diseases may affect multiple organ systems and include conditions such as systemic lupus erythematosus, juvenile idiopathic arthritis, and common variable immunodeficiency. Phenotype definitions found in this collection may use diagnosis codes, lab results (e.g., ANA titers, immunoglobulin levels), medication usage (e.g., biologics, steroids), and clinical specialty involvement (e.g., rheumatology, immunology). Example phenotypes include “Juvenile Idiopathic Arthritis,” often requiring a combination of diagnosis codes and rheumatology care, and “Primary Immunodeficiency,” which may involve repeated infections, genetic testing, and replacement therapy (e.g., IVIG).