Telomere dynamics link molecular and cellular mechanisms with organismal processes and therefore may explain variation in a number of important life-history traits. Telomere length has been used to estimate age in free-living populations of animals. Such estimation is a potentially powerful tool in the context of population dynamics and management, as well as the study of life-history trade-offs. The number of studies utilizing telomere restriction fragment assays in the fields of ecology and evolution is steadily growing. However, the field lacks methodological and analytical standardization resulting in considerable variation in telomere length and therefore in the usefulness of these techniques. Here, we illustrate new laboratory and analytical methods to reliably measure telomere length from blood erythrocytes and accurately assess the relationship between telomeres and age. We demonstrate the importance of analysing those telomeres most relevant to age-related studies: the shortest telomeres. We present a reliable method to quickly identify an analysis window (the telomere optimal estimate, TOE) which approaches the optimal window for age estimation. Because the TOE focuses on the shortest telomeres - those telomeres which signal cellular senescence and ageing - TOE can also be used to compare telomeres in age-matched individuals. We also compare constant- and pulsed-field gel electrophoresis to show how each can influence telomere measurement. The use of TOE should provide powerful telomere-based age estimation and enable organismal biologists to readily uncover individual and longitudinal differences with regard to telomere dynamics.