We report on a 16-year-old male patient with moderate intellectual disability, behavioral problems, and further anomalies such as facial dysmorphism, heart defect, and urogenital anomalies. By molecular karyotyping we identified the first de novo copy number gain to four copies on chromosome 17q21.31 including the MAPT gene but not the entire recurrent microdeletion/microduplication region. Recurrent microdeletions of this region including the MAPT and the CHRH1 genes have been shown to be a relatively frequent cause of intellectual disability, while only a few reciprocal duplications in patients with variable cognitive disorders have been published so far. A common inversion polymorphism in this region has been linked to a distinct H2 haplotype and seems to be associated with an increased risk for microdeletions and -duplications. Our patient and his father were both heterozygous for the H1/H2 haplotype, whereas the mother was homozygous for the H2 haplotype. In our patient the dosage gain apparently occurred on the paternal H1 allele and did not involve the H2 allele as in the previously published cases. This patient further delineates the genotypic and phenotypic variability associated with copy number variants from the 17q21.31 microdeletion region. © 2012 Wiley Periodicals, Inc.