These authors identified >4,000 candidate enhancers that are predicted to function in mouse craniofacial development. For three of these candidates they showed that deletions alter the expression of nearby genes that have known roles in craniofacial development. Using micro-computed tomography — a high-resolution three-dimensional imaging method — they accurately measured the skulls of mice that carried these mutations and found subtle but significant effects. These findings have implications for understanding the genetic bases of both normal and abnormal craniofacial morphology.