Intrinsic and extrinsic factors interact to produce variation in individual life history and aging trajectories. Telomeres are structures at the ends of eukaryotic chromosomes that serve critical roles in maintaining genome integrity. In the absence of active maintenance, telomeres shorten with age and serve as a marker of age-related functional declines. Variation in early life telomere length is associated with fitness traits such as reproduction and survival, allowing telomeres to provide insight into the long-term consequences of developmental environments. Here, we assess the influence of extrinsic and intrinsic factors on telomere dynamics in hatchling American alligators (Alligator mississippiensis) which were incubated under eight different experimental treatments. We measured telomere length and a panel of eight steroid hormones involved in glucocorticoid signaling and synthesis. We find that both extrinsic and intrinsic factors influence variation in hatchling telomere length. Incubation temperature and exposure to the contaminant DDE interacted to affect telomere length. Clutch was an important driver of variation in both telomere length and body size. Interestingly, body mass was negatively associated with telomere length both across and within clutches. We further examined the potential of glucocorticoid signaling to mediate organismal responses to extrinsic factors and found that contaminant exposure elicits increases in circulating levels of cortisol, which trends negatively, although not significantly, with telomere length. Together, these findings advance our understanding of how environmental factors interact with developing embryos to persistently affect telomere biology in a long-lived species.