Separation anxiety disorder can be difficult to diagnose because the symptoms of the disorder are similar to other conditions and there may be complicating factors such as trauma. The assessment will include acomplete medical history and physical exam to rule out medical conditions that include: mitral valve prolapse, diabetes, anemia, lead poisoning, and thyroid problems. Interviews will take place with your child to find out about his symptoms. The clinician is likely to assess for suicide ideation if the disorder is severe. Interviews with all family members may be necessary to obtain family history of anxiety or other mental disorders. Other caregivers may be asked to provide information if school refusal is an issue, for example, teachers. The clinician will need to know when your child's symptoms began, their development, and in what situations your child is struggling to aid in diagnosis. Clinical information regarding family dynamics is important to assess if the interactions with your child are unwittingly increasing your child's anxiety.

Other assessments include a comprehensive family interview assessment that examines family dysfunction and communication styles. The clinician will want to find out if precipitating factors have occurred such as losses, major life transitions, or traumas. Family patterns of relating to one another are important to determine what dysfunction is present, for example, if the child and parent are enmeshed.