Telomerase activity and telomere length (TL) are prognostic markers in chronic lymphocytic leukemia (CLL). The rate-limiting component of telomerase is human telomerase reverse transcriptase (hTERT), for which multiple transcripts exist. Two splicing sites, α and β, have been described that generate deleted transcripts. Only the full-length (FL; α⁺β⁺) transcript translates into a functional protein. The aim of this work was to characterize hTERT splice variants in CLL in relation to disease activity, clinical stage, immunoglobulin heavy chain variable (IGHV) genes mutational status, and TL. Real-time polymerase chain reaction assays were validated for quantification of the hTERT transcripts with either α deletion (del-α; α⁻β⁺)), β deletion (del-β; α⁺β⁻) or both α and β deletions (del-αβ; α⁻β⁻). The splice variant expression pattern was studied in 97 patients with CLL, 6 healthy control subjects, and one CD34 cell sample. TL was assessed with real-time polymerase chain reaction in 71 of 97 samples. Thirty-two percent of the cases did not express any of the splice variants. Average FL expression was 5.5-fold higher in IGHV-unmutated (n = 35) compared with mutated (n = 59) patients (p < 0.0001). FL levels correlated directly with the percentage of IGHV homology (r = 0.34; p = 0.0007) and inversely with TL (r = -0.44; p = 0.0001). Overall, FL expression correlated significantly with that of the other splice variants. All transcripts were more frequently expressed in progressive compared with nonprogressive patients (p < 0.0001 for FL and del-α; p = 0.01 for del-β; and p = 0.006 for del-αβ). This study provides a detailed insight into the hTERT transcript pattern in CLL, highlighting the necessity of subgrouping patients according to IGHV mutation status when analyzing hTERT expression.