OBJECTIVE To investigate the prognostic value of thrombocytopenia in patients with primary myelodysplastic syndromes (MDS). METHODS Four hundred and nineteen primary MDS patients were retrospectively analyzed. Kaplan-Meier method, Log-rank test and COX regression model were used to evaluate factors that influence the prognosis. RESULTS Two hundred and fifty-six cases (61.1%) had thrombocytopenia (PLT < 100×10(9)/L), one hundred and three cases (24.6%) had severe thrombocytopenia (PLT < 30×10(9)/L). Overall survival (OS) tended to shorten along with the decreasing of platelet count. Univariate analysis indicated that PL < 30×10(9)/L, MCV ≤ 95 fl, LDH ≥ 300 U/L, lymphocyte-like micromegakaryocyte, nucleated RBC PAS positive, IPSS cytogenetic intermediate- and poor-risk were all related with poor prognosis. Moreover, the prognosis of patients with RCMD, RAEB-Ior RAEB-IIwas poorer than that of the other subgroups. Among these parameters, PLT < 30×10(9)/L, MCV ≤ 95 fl, IPSS cytogenetic intermediate- and poor-risk group and RCMD, RAEB-I and RAEB-II had independent prognostic significance in multivariate analysis. Modified WPSS prognostic model was proposed by adopting PLT, MCV, chromosomal karyotype and WHO classification. The OS of patients with low risk, intermediate-1 risk, intermediate-2 risk and high risk were 59, 28, 14 and 4 months, respectively, and there was a statistically significant difference between the groups (P < 0.05). CONCLUSIONS Severe thrombocytopenia indicated unfavorable prognosis, in combination with MCV, chromosomal karyotype and WHO classification, a modified WPSS prognostic model was proposed and worked well for prognostic indication in patients with MDS.