Naevoid basal cell carcinoma syndrome (NBCCS) or Gorlin syndrome is a rare autosomal dominant cancer disorder. The Gorlin's gene, Patched 1 (PTCH1), maps to Chromosome 9q. Germline mutations of PTCH1 occur in patients with NBCCS. The subsequent loss of the remaining allele results in cancer formation. We present a patient with NBCCS and additional phenotypic features including severe developmental delay, short stature and hypotelorism who was found to have an interstitial chromosome 9q deletion. The NBCCS phenotype in our patient occurred as a result of PTCH1 deletion in contrast with an inherited mutation of this gene.