Coffin–Lowry syndrome (CLS) is a rare genetic disorder inherited in an X-linked dominant pattern. Common manifestations include intellectual disability, growth retardation, dysmorphic facial features, and variable skeletal anomalies. Here we report a patient who first presented with episodes of apparent life-threatening events (ALTE) found to be caused by hydrocephalus and brainstem compression at the foramen magnum. Together with his small size, short limbs and fingers, and facial appearance, the narrowing of the foramen magnum lead to the initial clinical misdiagnosis of hypochondroplasia. Subsequent evaluation and testing lead to the correct diagnosis of CLS. This case demonstrates the variability in presentation of CLS, and that skeletal findings may be misleading in infancy. © 2017 Wiley Periodicals, Inc.