We report a 4 2/12-year-old Japanese boy with a de novo direct tandem dup (4) (q25q31.3). The major clinical picture includes postnatal growth and psychomotor retardation, thick eyelashes, a cleft lip, and large and prominent helix and antitragus. He did not have any hearing deficit. His eyegrounds were normal. There was no organ malformations including brain, kidney, liver, pancreas, gallbladder, urinary bladder, stomach, and heart. Routine hematological tests, blood chemistry including thyroid hormones, and urinalysis including urinary screening tests for congenital metabolic disorders showed normal results. He showed an electroencephalographic abnormality which could have resulted from mild aseptic meningitis at 2 months. Our case supports the idea that the association of thumb and renal deformities in duplication 4q syndrome is related to the region 4q22-q23 as many researchers have already pointed out.