We report on a girl with an abnormal hybridization pattern for the subtelomeric fluorescence in-situ hybridization (FISH) probe panel showing deletion of the long arm telomeric region of chromosome 6. All other subtelomere DNA probes showed normal hybridization patterns. Metaphase cells analysed from cultures of peripheral blood revealed a normal female chromosome complement at the 650-band level. The deletion was further characterized using genomic microarray analysis. Clinical findings include: developmental delay, seizures, hypoplasia of the corpus callosum, dextrocardia, unusual dimpling of knees and elbows, and minor anomalies. We are aware of only two other reports of isolated cryptic 6q subtelomeric deletions not associated with other chromosomal abnormalities. The absence of retinal abnormalities in our case supports the theory that genes responsible for the retinal abnormalities in other terminal 6q deletions are proximal to 6q27. Subtelomeric FISH probes were useful in establishing a diagnosis in our patient. As more cases are reported, we may be able to establish discrete phenotypes and natural histories that can aid in counselling families.