Telomeres shorten with each cell division and telomere dysfunction is a recognized hallmark of aging. Tissue proliferation is expected to dictate the rate at which telomeres shorten. We set out to test whether proliferative tissues age faster than non-proliferative due to telomere shortening during zebrafish aging. We performed a prospective study linking telomere length to tissue pathology and disease. Contrary to expectations, we show that telomeres shorten to critical lengths only in specific tissues and independently of their proliferation rate. Short telomeres accumulate in the gut but not in other highly proliferative tissues such as the blood and gonads. Notably, the muscle, a low proliferative tissue, accumulates short telomeres and DNA damage at the same rate as the gut. Together, our work shows that telomere shortening and DNA damage in key tissues triggers not only local dysfunction but also anticipates the onset of age-associated diseases in other tissues, including cancer. Why, and how, organisms age and ultimately die is a key question of modern biology. Telomeres are considered molecular timekeepers determining cellular lifespans. Within an organism, tissue proliferation is expected to dictate the rate at which telomeres shorten. Using zebrafish, an organism with human-like telomeres, we set out to test whether, in natural aging, proliferative tissues age faster than non-proliferative in a telomere-dependent manner. We found that telomeres shorten with age to a level where they trigger telomere associated DNA damage and culminate in tissue dysfunction, independently of high or low tissue proliferation rates. Specifically, short telomeres accumulate in the gut, a highly proliferative tissue, and in the muscle, a low proliferative tissue, working as direct predictors of cellular damage prior to onset of intestinal inflammation and myocyte degeneration. Based on our data, we propose a model where telomere shortening in these key tissues is sufficient to trigger damage in others and precedes the onset of organism age-associated diseases, namely cancer. Thus, tissue-specific telomere length is limiting for local and systemic physiological integrity, leading to tissue degeneration and disease in aging.