Relatively little is known about 7q terminal deletion contiguous gene deletion syndrome. The deleted region includes more than 40 OMIM genes. We here report on a 13-year-old boy with 7q terminal deletion syndrome, a 6.89-Mb sized deletion on 7q36.1q36.3, identified by oligonucleotide array comparative genomic hybridization (CGH). He showed microform holoprosencephaly with microcephaly, distinctive facial features, severe intellectual disabilities, behavior problems, seizures, short stature, penoscrotal transposition, and ulnar ray deficiency. To date, no case of penoscrotal transposition or ulnar ray deficiency has been reported in 7q terminal syndrome. The majority of our patient presentations were attributed to dosage expression of the SHH gene with contributions from deleted genes within 7q.