Crocodilians in aquacultural settings exhibit variations in growth and condition. The underlying cause of this has yet to be elucidated, but corticosterone (CORT, the main crocodilian stress hormone) is thought to play a role in this. In this study, we measured baseline plasma CORT, heterophil-lymphocyte (H/L) ratios, relative glucocorticoid receptor (GR) levels in the forebrain, and body condition index (BCI) of juvenile American alligators (Alligator mississippiensis). Both univariate and multivariate analyses were used to investigate underlying relationships. In univariate analysis, BCI was negatively related with GR levels, but not by plasma CORT. Multivariate analysis revealed that both relative forebrain GR levels and plasma CORT were negatively related with alligator BCI: alligators with higher body condition had lower levels of CORT and GRs. However, H/L ratios were unrelated to BCI. Our results implicate dysregulation of the hypothalamic-pituitary-adrenal axis as an important factor influencing crocodilian body condition.