Ectrodactyly-ectodermal dysplasia-clefting (EEC) syndrome associated with a paracentric inversion of chromosome 7 in a 2-year-old Japanese girl is reported. She had sparse and light-brown hair, bilateral cleft lip and palate, fused lower incisors, a pigmented skin lesion at the neck, accessory nipples, limited extension of elbow joints and bilateral ectrodactyly of hands and feet. Cytogenetic studies demonstrated a balanced inv(7)(q22.1;q36.3) in the patient and her father. The association of EEC syndrome and inv(7) in the patient suggested a putative locus of the EEC syndrome gene either at 7q22.1 or 7q36.3, although a coincidental occurrence of the two conditions is an alternative explanation. A comparison with reported karyotypes in patients with EEC or isolated ectrodactyly favoured 7q22.1 as the locus. A normal phenotype of the father in our family might reflect reduced penetrance of the EEC syndrome or, possibly, reduced expression of a maternally-derived allele of the EEC syndrome gene through a genomic imprinting mechanism.