The COVID-19 pandemic has not only reshaped human health through its acute effects but has also induced long-term consequences, particularly in emerging autoimmune diseases. This introduces the concept of Immune-Repertoire Alteration Syndrome (IRAS), a post-infectious autoimmune phenotype, which describes how pathogen-induced changes in the immune system lead to lasting predispositions for autoimmune disorders. The immune system’s adaptive response to infection, including modifying T-cell repertoires, may inadvertently result in autoimmunity due to cross-reactivity with self-antigens. This phenomenon, referred to as pathogen-induced autoimmune imprinting, leaves a persistent “scar” on the immune system, predisposing individuals to autoimmune diseases long after the initial infection has resolved. This highlights how SARS-CoV-2 and similar pathogens can initiate this process, altering immune responses in a way that may trigger conditions such as autoimmune thyroid disease, lupus, and vasculitis. Additionally, the concept of antigenic imprinting explains how infections and vaccinations influence the immune system’s future responses, often leading to mistaken recognition of self. Finally, the Human Disease Continuum Project (HDCP) is introduced as a research initiative that aims to decode the links between pathogen exposure and autoimmune disease susceptibility. Through comprehensive immune profiling and longitudinal studies, the HDCP seeks to unravel the molecular and immunological mechanisms that underlie these diseases, paving the way for early detection, prevention, and personalized treatment strategies in the post-COVID-19 era. Understanding autoimmune imprinting will unravel new avenues for precision medicine and provides critical insights into the long-term impact of global pandemics on human health.