By identifying structural chromosome anomalies, the clinical cytogenetics laboratory can play a critical role in the diagnosis and treatment of patients with birth defects. Although many new staining techniques have been developed throughout the years to aid in the detection of anomalous chromosomes, some abnormalities still pose a special challenge to cytogeneticists. This difficulty is especially evident in patients with an abnormal chromosome that does not produce a recognizable banding pattern by conventional staining techniques. We describe a recently discovered method of identifying chromosomes by using whole chromosome-specific DNA probes and fluorescent in situ hybridization and provide examples of how this new procedure facilitated the identification of chromosome abnormalities in two patients with multiple birth defects.