Clinical diagnosis of PJS is based on the mucocutaneous findings and the histologic appearance of the polyps, which exhibit a unique microscopic morphology, with mucosa interdigitating with smooth muscle fibers to form a characteristic arborizing pattern. A definite diagnosis of PJS can be established by the presence of histopathologically confirmed hamartomatous polyps and two of the following clinical criteria: family history, hyperpigmentation, and small bowel polyposis. A probable diagnosis is based on the clinical findings in the absence of histologic confirmation of hamartomatous polyps. To confirm the diagnosis, genetic testing may be used, as screening for the LKB1 mutation is commercially available.

The differential diagnosis of PJS includes juvenile polyposis (polyposis without the hyperpigmented macules), Cronkhite-Canada syndrome (polyposis and cutaneous hyperpigmentation, but no mucosal lentigines), and Laugier-Hunziker syndrome (mucocutaneous hyperpigmentation without gastrointestinal polyps).

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