A high percentage of patients with DiGeorge syndrome and velo-cardio-facial syndrome have interstitial deletions on chromosome 22q11. The shortest region of overlap is currently estimated to be around 55 kb. Two segments of DNA from chromosome 22q11, located 160 kb apart, were cloned because they contained NotI restriction enzyme sites. In the current study we demonstrate that these segments are absent from chromosomes 22 carrying microdeletions of two different DiGeorge patients. Fluorescence in situ and Southern blot hybridization was further used to show that this locus is within the DiGeorge critical region. Phylogenetically conserved sequences adjacent to one human cell lines. cDNAs isolated with a probe from this segment showed it to contain the gene for teh human mitochondrial citrate transporter protein. Deletion of this gene in DiGeorge syndrome and velocardio-facial syndrome may contribute to the mental deficiency seen in the patients.