The myelodysplastic syndrome (MDS) is a group of hematopoietic stem cell-clonal disease. The International Prognostic Scoring System (IPSS) is mainly used for its prognostic classification, but still remains some unrepeatable results in the same group of patients with MDS. This study was aimed to compare the levels of peripheral blood mean corpuscular volume (MCV), serum lactate dehydrogenase (LDH), β2-microglobulin (β2-MG), ferroprotein (SF), Vit B12 in patients with MDS classified by IPSS and to explore the relationship between the prognosis and laboratory indexes above mentioned in MDS patients. 116 patients with MDS were divided into 4 group: low-risk, intermediate risk-I, intermediate risk-II and high-risk according to IPSS. The index of MCV, serum LDH, β2-MG, SF and Vit B12 in MDS patients prior treatment and in normal control group were detected. Data with normal group and each groups of MDS were compared. The results showed that the levels of MCV, LDH, β2-MG, SF were Vit B12 in patients with MDS were significantly higher than those in normal control group (P < 0.05). There were significant differences of serum LDH among the 4 groups of MDS (P < 0.05), and the levels of serum LDH increased in turn: low-risk, intermediate risk I, intermediate risk II and high-risk. Serum β2-MG level in the high-risk group was significantly higher than that in the groups of low risk, intermediate risk I and intermediate risk II (P < 0.05), the difference among the latter three groups was not statistically significant (P > 0.05). There were no significant differences in MCV, SF and Vit B12 levels of all groups compared with each other. It is concluded that the level of serum LDH and β2-MG seems to have a certain correlation with the progress and prognosis of the MDS, which may be useful for predicting the prognosis of the MDS besides IPSS scoring system.