Cystinosis is a recessive genetic metabolic disorder in which the amino acid cystine accumulates in various organs of the body. Previous studies have demonstrated visuospatial dysfunction in children and adults with this disorder. It is not known whether this is a result of the genetic alteration or an accumulation of cystine in the brain over time. This study investigated patterns of performance in 20 young children with cystinosis (4–7 years) and 20 matched controls on the Wechsler Preschool and Primary Scale of Intelligence-Third Edition (WPPSI-III). The children with cystinosis had a mean Full Scale IQ at the low end of the average range. Their overall cognitive functioning was comprised of average verbal abilities, low average non-verbal abilities, and low average processing speed. Multivariate analyses indicated that the cystinosis and control groups were not significantly different on the verbal subtests. In contrast, the cystinosis group performed significantly more poorly than controls on the performance and processing speed subtests. Although overall intellectual function was in the normal range, young children with cystinosis demonstrated a discrepancy such that non-verbal abilities were poorer relative to verbal abilities. This pattern resembles the cognitive profile found previously in older individuals with cystinosis and indicates that the specific cognitive profile emerges early in development. These findings suggest that the cognitive dysfunction in cystinosis is not merely the result of cystine accumulation over time but may be related to differences in brain development as a consequence of alterations or deletions of the cystinosin gene. © 2007 Wiley-Liss, Inc.