Deborah Waber's research goal is to investigate in a developmental context the influence of exogenous and endogenous factors on children's neurobehavioral functioning. She and her colleagues have examined the impact of childhood cancer (acute lymphoblastic leukemia and brain tumors) and its therapies on long-term neurodevelopmental outcomes in children who survive these diseases. In collaboration with the Dana-Farber Cancer Institute Acute Lymphoblastic Leukemia Consortium, the Waber group has tracked late neurocognitive effects associated with therapies for acute lymphoblastic leukemia. Their studies have documented a steady reduction of adverse long-term effects, over a 20-year period, even as the efficacy of therapies improved.

Waber and colleagues also investigate idiopathic learning disabilities, particularly low-level information processing problems. In studies of children referred for learning problems, they have documented that a decreased efficiency of low-level information processing is independent of academic skill levels. Waber's research suggests that learning disability is better understood as a developmental disorder than as a deficit in academic skills.