We report on a 5-year-old boy with minor anomalies, growth retardation, and developmental delay carrying an extra chromatin material on the terminal band of the long arm of chromosome 6. To determine the origin of this extra material, whole chromosome fluorescence in situ hybridization (FISH) was used initially. Results showed fully painted 6qs, excluding the possibility of a derivative. However, maternal cytogenetic investigation suggested the presence of a possible half-cryptic balanced translocation that was further assessed using specific subtelomeric FISH probes of chromosome 6. Results showed that the 6q subtelomeric region was translocated on an A-group chromosome that was ultimately characterized, using FISH, as chromosome 2. This illustrates the use of specific subtelomeric regions and the limitations of whole chromosome FISH to identify the origin of a subtle chromosomal abnormality.