Telomeres are specialized structures maintaining chromosome integrity during cellular division and preventing from premature senescence and apoptosis. The rate-limiting component of telomerase is human telomerase reverse transcriptase (hTERT), for which multiple transcripts exist. The aim of this work was to characterize hTERT splice variants in MDS and its relation to telomerase activity, telomere length and hTERT expression. The telomere length in PBMCs of patients with MDS cases was significantly shorter compared to controls (n=30, p=0.002). MDS patients had significantly higher basal telomerase activity (p=0.022) and higher total hTERT (p=0.007), α+β+ hTERT variant (p=0.016) and α+β- hTERT variant expression than control. The ratio of α+β- transcript to α+β+ transcript was significantly increased in cases (p=0.039). This study provided a detailed insight into the hTERT transcript pattern in MDS while correlation analysis showed that only telomerase activity was significantly correlated with total hTERT expression in MDS.