Cytogenetics is a major predictor of disease behavior and treatment outcome in myelodysplastic syndromes (MDS). Deletion of the long arm of chromosome 5, del(5q), is the most common chromosomal abnormality found in patients with MDS. The development of lenalidomide (Revlimid; Celgene, Summit, NJ) as an effective targeted therapy for low/intermediate-risk MDS with a del(5q) has increased the importance of karyotyping in disease management. In the present review, the importance of an accurate cytogenetic diagnosis in del(5q) MDS, its impact on prognosis, and the effect it can have on the choice of treatment was discussed. In addition, the strengths and limitations of conventional and novel cytogenetic testing techniques currently available for patients with del(5q) MDS were evaluated. A practical diagnostic algorithm was provided to help facilitate the early detection and optimal treatment of MDS patients with a del(5q) abnormality. While the gold standard for genetic testing remains metaphase karyotyping, emerging novel molecular techniques such as fluorescence in situ hybridization may provide clinically valuable complementary and supplemental data.