Alterations in telomere dynamics both suppress and facilitate malignant transformation by regulating genomic stability and cell lifespan. Checkpoints induced by telomere dysfunction play a major role in tumour suppression, whereas telomere shortening contributes to the initiation of cancer by inducing chromosomal instability. Since stem cells are exposed to various tumourigenic agents and stresses throughout their lifetime, the ageing stem cell is a major target of malignant transformation. This review summarises our knowledge of telomere length and telomerase activity in stem cells during ageing and carcinogenesis.