Autoimmune diseases, such as systemic lupus erythematosus and rheumatoid arthritis, are said to be “complex” diseases, but what does “complex” really mean? The answer can mean different things depending on the context. At the genetic and molecular level, “complex” can mean environmental triggers working in conjunction with an individual’s genetic make up to stimulate the onset of disease. To the patient with autoimmune disease, “complex” can mean years of undiagnosed symptoms and medical testing before a diagnosis is made followed then by years of intensive immunosuppressive therapy. The work in our laboratory is focused on understanding the complexity of genetic diseases so that patients can lead healthier, happier lives. To do this, we use modern genetic analysis technologies including high throughput genotyping and genomic sequencing coupled with functional molecular analyses to discern the pathway from genotype to phenotype. Ultimately, we hope this work will lead to a more precise mechanistic understanding of autoimmune disease pathology and open new therapeutic hypotheses for drug discovery.