We report on a patient with an interstitial 6q deletion presenting with moderate mental retardation, persisting hypotonia, facial dysmorphism, but no internal malformations. Standard cytogenetic analysis identified a de novo interstitial 6q deletion. Molecular karyotyping using a 1 Mb array estimated the size of the deletion at approximately 14 Mb encompassing band q16 of chromosome 6. This case report illustrates how the molecular delineation enables improved genotype-phenotype correlations of chromosomal abnormalities to be made and may improve medical care and genetic counselling in individuals with chromosomal imbalances.