SummaryIn patients with myelodysplastic syndromes (MDS), sole 20q deletion [del (20q)] is a recurrent favourable abnormality. We studied additional molecular and cytogenetic lesions and their prognostic impact in 305 MDS patients with del(20q) (229 males/76 females; 29-90 years). All patients were investigated by cytomorphology and chromosome banding analysis (CBA), subsets by fluorescence in situ hybridization, molecular mutation screening, and array comparative genomic hybridization (aCGH). By aCGH (n = 30), the minimal common deleted region (CDR) was flanked by PTPRT (20q13Á11) and EYA2 (20q13Á12). 210 (68Á9%) patients had 'early MDS' without blast increase, 95 (31Á1%) 'advanced' MDS with blast increase (5-19%). Additional chromosomal abnormalities (ACAs) were detected in 88/305 (28Á9%) patients. Patients with advanced MDS more frequently had ACAs (P = 0Á003) and had a higher mean number of ACAs (P = 0Á020) and of molecular mutations (P = 0Á060). Spliceosome mutations were frequent (U2AF1: n = 31/ 155; 20Á0%; SRSF2: n = 31/159; 19Á5%; SF3B1mut: n = 8/159; 5Á0%). ASXL1-mut (25/153; 16Á3%) were associated with advanced MDS (P = 0Á001). Presence of ≥3 ACAs (P = 0Á003) and ASXL1mut (P = 0Á002) were associated with worse 2-year survival. In conclusion, the cytogenetic subgroup of MDS with del(20q) has a good prognosis but may be further subclassified by additional cytogenetic and molecular lesions. U2AF1mut is overrepresented in MDS with del(20q), and ASXL1mut is prognostically adverse.