Neuronal ceroid lipopofuscinosis (Batten disease, NCL) represents a group of common childhood neurodegenerative diseases with a shared feature of deposition of abnormal metabolic products in neurons and other tissues, including peripheral blood lymphocytes. In most forms of NCL no specific enzyme defect is known and the diagnosis relies primarily on ultrastructural identification of characteristic membrane-bound inclusions containing the abnormal metabolic product. All buffy-coat specimens examined during a 7-year period (1997-2004) for the exclusion or confirmation of the diagnosis NCL were reviewed. From a total of 265 samples, 9 were inadequate and NCL was diagnosed in 56. Five showed granular osmophilic deposits of infantile Batten disease (NCL1), 10 showed curvilinear profiles of classical late infantile Batten disease (NCL2), and 17 showed vacuolated lymphocytes with fingerprint profiles, indicating classical juvenile Batten disease (NCL3). 24 samples (43%) demonstrated compact electron-dense deposits with fingerprint profiles in the absence of vacuolated lymphocytes, indicative of variant forms NCL. Ultrastructual examination of peripheral blood allows reliable and specific diagnosis of subtypes of Batten disease, including variants, and is a useful, minimally invasive test for the diagnosis of NCL in childhood.