Objective: Short telomere length is a known risk factor for developing clonal haematopoietic stem cell disorders, probably due to chromosomal instability. We tested the hypotheses that bone marrow mononuclear cell telomere length change from diagnosis through chemotherapy-induced remission and relapse, and that long telomere length is associated with low risk of relapse and all-cause mortality in patients with acute myeloid leukaemia or high-risk myelodysplastic syndrome. Methods: We measured telomere length in bone marrow mononuclear cells from 233 patients at diagnosis, 112 patients at chemotherapy-induced remission and 58 patients at relapse of disease. Results: In patients with acute myeloid leukaemia or high-risk myelodysplastic syndrome, bone marrow mononuclear cell telomere length was similar at diagnosis and relapse, but increased after chemotherapy-induced remission. Furthermore, bone marrow mononuclear cell telomere length was longer in patients with higher age at diagnosis. There was no association between telomere length at diagnosis, remission or relapse and all-cause mortality, nor did we find any association between telomere length at diagnosis or remission and risk of relapse. Conclusion: In patients with acute myeloid leukaemia or high-risk myelodysplastic syndrome, bone marrow mononuclear cell telomere length increased from diagnosis to remission. Furthermore, telomere length paradoxically was longer at higher age at diagnosis, even after adjusting for known risk factors of disease severity. Finally, we did not detect any prognostic information in telomere length.