Uncertainty in the diagnosis of abuse can have profound implications for the health and safety of the child, the emotional burden of a family, and investigative and criminal proceedings. A logical algorithm for addressing physical and sexual abuse cases that details aspects contributing to the uncertainty may aid the clinician in making a diagnosis and in communicating the crucial details to the relevant investigative agencies. This article defines and discusses uncertainty in the realms of physical and sexual abuse, and suggests an approach to managing uncertainty while still providing valuable information for the medical and child protective service systems.