Cytopenia is a common problem in hematology outpatient clinics and among hospitalized patients. A bone marrow (BM) aspirate and biopsy are often performed to rule out an infiltrative versus intrinsic BM process, such as myelodysplastic syndrome (MDS). We have previously described a flow cytometric (FCM) assay useful in diagnosing MDS and demonstrated its good correlation with "gold standard" morphologic and cytogenetic criteria. In this study, we prospectively tested the utility of the FCM assay in 102 cytopenic patients with BMs showing neither diagnostic morphological dysplasia nor abnormal cytogenetics. FCM, following our published criteria, was positive in 22 cases (21.6%), intermediate in 11 cases (10.8%) and negative in 69 cases (67.6%). With a median follow-up period of 11 months (range, 4-24 months), 12 (11.8%) patients were proven to have or/develop MDS or related BM diseases (group-1); 61 (59.8%) patients had their cytopenia(s) attributed to various medical causes (group-2). In the remaining 29 patients, the causes of cytopenia(s) were not found, and some had the features consistent with the recently defined clinical entity -- idiopathic cytopenia of uncertain significance. A positive FCM result was significantly more prevalent (9/12, 75%) in group-1 patients; while a negative FCM result was significantly more frequent in group-2 patients (4/61, 7%) (p<0.0001) with a positive predictive value of 69% and a negative predictive value of 95%. We conclude that FCM analysis of myelomonocytic maturation has diagnostic utility in cytopenic patients who have an inconclusive BM examination by morphologic and cytogenetic evaluation, and may therefore be a useful adjunct in clinical management of these patients.