Dr. Caughey's clinical and research interests incorporate methodology from clinical epidemiology, biostatistics, health economics, health policy and the decision sciences to examine questions in prenatal screening and diagnosis of birth defects and genetic disorders, how the management and outcomes of pregnancies change by week of gestation, the risks and benefits of various modes of delivery, including spontaneous vaginal delivery, operative vaginal delivery, and cesarean delivery, and the epidemiology and outcomes related to diabetes in pregnancy.

His work in these three areas has led to more than 300 original authored or co-authored manuscripts.