Because Alagille syndrome can affect many organ systems, and because severity differs enormously from person to person, doctors rely on a set of five characteristic features to make and confirm a diagnosis rather than looking for one single defining sign.
• Hepatic: a reduced number of small bile ducts within the liver combined with impaired bile flow, known as cholestasis, seen on liver biopsy in about ninety-five percent of affected individuals.
• Cardiac: congenital heart defects, most commonly narrowing of the peripheral pulmonary arteries, found in roughly ninety to ninety-seven percent.
• Skeletal: butterfly-shaped vertebrae in the spine, usually in the chest region, seen on an x-ray in a wide range of thirty-three to ninety-three percent of individuals.
• Ophthalmologic: a distinctive ring-shaped structure at the front of the eye called posterior embryotoxon, present in seventy-eight to eighty-nine percent and usually only found on a careful eye examination.
• Facial: characteristic features including a broad forehead, deep-set eyes, a straight nose with a bulbous tip, and a pointed chin.

Beyond these five defining features, many individuals also have additional findings:
• Kidney abnormalities, in about thirty-nine percent
• Blood vessel abnormalities, including a risk of bleeding inside the skull, in fifteen to thirty percent.
• Poor growth, affecting fifty to ninety percent.
• Developmental delay or difficulty with attention and planning skills.
• An enlarged spleen.
• Intense itching, in about seventy-four percent of children, and fatty skin deposits called xanthomas, in about twenty-four percent, both related to the buildup of bile acids in the skin.

A clinical diagnosis is made when a person has bile duct reduction on liver biopsy together with at least three of the other four major features, or when a person has only one major feature but has a parent or sibling already confirmed to have Alagille syndrome. Because clinical findings can be subtle or absent in infancy, genetic testing of the JAG1 and NOTCH2 genes is used to confirm the diagnosis, most often through sequence analysis of JAG1 first, followed by deletion or duplication testing, and NOTCH2 testing if suspicion remains high after JAG1 testing is negative.

Each individual with Alagille syndrome presents the condition differently, symptoms observed in one may not manifest in others.