Raychaudhuri has used genetics, genomics, and human immunology to define the basis of rheumatoid arthritis and other immune-mediated diseases. He is one of the leaders of the International Genetics of Rheumatoid Arthritis consortium, which has identified over 100 risk alleles. He has also been at the forefront of devising statistical and computational methods to localize genetic association signals to causal variants, and to interpret human genetic data in the context of functional information. Raychaudhuri currently has active research programs in the human genetics and functional genomics of tuberculosis, type I diabetes, and rheumatoid arthritis, with a specific focus on using single cell genomic strategies to understand tissue inflammation and the role played by CD4+ T cells and fibroblasts. He is a member of the IGVF, ITN, and AMP AIM consortia. He is the recipient of the Doris Duke Clinical Scientist Development Award and the Henry Kunkel Young Investigator award from the American College of Rheumatology, and he is a member of the American Society for Clinical Investigation and a fellow of the American Association for the Advancement of Science.