Klinefelter syndrome is a common condition that remains underdiagnosed, particularly prior to adulthood. Early detection could prevent morbidity and mortality, but the classic phenotype of small testes and tall stature may not be apparent until adolescence, and there is minimal guidance regarding whom to screen. We performed a retrospective study at Boston Children's Hospital in patients with the ICD-9 code for "Klinefelter syndrome" diagnosed prior to age 20 years, and determined age and reason for diagnosis, karyotype, heights, and comorbid conditions. Eighty percent had a 47,XXY karyotype, of whom half were diagnosed at age 11 to 19 years. The most common comorbidities were neurocognitive, including learning disabilities (67%), psychosocial problems (33%), and attention deficit disorder (27%). Subjects were only slightly taller than average in childhood (height standard deviation score = 0.64). These data show that Klinefelter syndrome is associated with long-standing comorbidities that frequently remain under-recognized; a karyotype should be considered in boys with neurocognitive problems.