Diagnosis of myelodysplastic syndromes (MDS) relies on well-defined cytomorphologic criteria but is challenging in a significant number of patients. The detection of aberrant antigen expression by multiparameter flow cytometry (MFC) is considered a promising tool to improve MDS diagnostics. We prospectively analyzed 804 unselected patients sent with suspected MDS for correlation of MFC findings with overall survival (OS) in the context of cytomorphologic and cytogenetic findings. Patients with evidence of MDS by MFC had a significantly worse OS as compared to those without (OS at 2 years, 71.2% vs. 89.4%; p<0.001). The number of aberrantly expressed antigens as a continuous variable was significantly associated with OS (p<0.001, HR 1.19 per additional aberrantly expressed antigen). Multivariate analysis proved a diagnosis of MDS by MFC to be independently associated with OS (p=0.050; HR 1.42). Further, a diagnosis of MDS by MFC was related to inferior survival within all three cytomorphologically defined subgroups, i.e. proven MDS (median OS, 45.4 vs. 52.8 months, p<0.001), suspected MDS (2-year-OS 75.0% vs. 82.8%; p=0.062) and MDS excluded (2-year-OS 63.5% vs. 92.8%, p=0.020). Our data clearly demonstrate that in the assessment of cytopenic patients with suspected MDS a diagnosis of MDS by MFC is independently associated with OS which had been been shown in previous studies for today's standard diagnostic parameters cytomorphology and cytogenetics. MFC may therefore be considered an additional tool in the diagnostic work-up of patients with suspected MDS.