His research into rare autoimmune brain diseases led to the invention of the HITS-CLIP method to study RNA regulation, and he is developing ways to explore the regulatory portions—known as the "dark matter"—of the human genome.

He was the first to definitively demonstrate that naturally occurring tumor immunity in humans was caused by antigen-specific cytotoxic (CD8+) T cells, helping to generate the foundation for the field of immuno-oncology.

[14] His laboratory went on to prove this hypothesis, demonstrating cdr2-specific CD8+ T cells were present in the peripheral blood[10] and cerebrospinal fluid[15] of patients with paraneoplastic cerebellar degeneration associated with tumor immunity to breast or ovarian cancers.

The discovery of that the Nova PND antigen (associated with paraneoplastic opsoclonus-myoclonus ataxia) was the first of a class of neuron-specific RNA-binding proteins led his laboratory to question the nature of RNA regulation in the brain and why it might be co-opted in cancer cells.

[27] After securing a $100M philanthropic grant for NYGC[28] and a seven-year Research Program Award from NINDS,[3] Darnell returned to pursue his work on genomic medicine and neuroscience at the Rockefeller University and HHMI in 2017.