A patient with Prader-Willi syndrome showed an elongated proximal 15q, and thus was initially considered to be negative for a proximal 15q deletion. However, repeated high resolution chromosome study demonstrating the DNA-replication banding patterns revealed an obvious deletion/deficiency of the 15q12 equivalent band on that elongated chromosome 15. This deletion was further verified by comparison with the parental chromosomes 15 and the deleted chromosome 15 was of paternal origin. The elongation was due to a long variant of 15q11.2 band, which has previously been shown to be polymorphic/variable. This variable proximal 15q site could potentially mask a deletion if it is too long, or mimic a deletion if it is too short. The use of the DNA-replication banding technique instead of the more widely used trypsin banding technique could alleviate this possible pitfall.