BACKGROUND: Cortisol and dehydroepiandrosterone (DHEA) are considered to be valuable markers of the hypothalamus-pituitary-adrenal (HPA) axis, while salivary alpha-amylase (sAA) reflects the autonomic nervous system. Past studies have found certain diurnal patterns among these biomarkers, with some studies reporting results that differ from others. Also, some past studies have found an association among these three biomarkers while other studies have not. This study investigates these patterns and associations in older adults by taking advantage of modern statistical methods for dealing with non-normality, outliers and curvature. Basic characteristics of the data are reported as well, which are relevant to understanding the nature of any patterns and associations. METHODS: Boxplots were used to check on the skewness and presence of outliers, including the impact of using simple transformations for dealing with non-normality. Diurnal patterns were investigated using recent advances aimed at comparing medians. When studying associations, the initial step was to check for curvature using a non-parametric regression estimator. Based on the resulting fit, a robust regression estimator was used that is designed to deal with skewed distributions and outliers. RESULTS: Boxplots indicated highly skewed distributions with outliers. Simple transformations (such as taking logs) did not deal with this issue in an effective manner. Consequently, diurnal patterns were investigated using medians and found to be consistent with some previous studies but not others. A positive association between awakening cortisol levels and DHEA was found when DHEA is relatively low; otherwise no association was found. The nature of the association between cortisol and DHEA was found to change during the course of the day. Upon awakening, cortisol was found to have no association with sAA when DHEA levels are relatively low, but otherwise there is a negative association. DHEA was found to have a positive association with sAA upon awakening. Shortly after awakening and for the remainder of the day, no association was found between DHEA and sAA ignoring cortisol. For DHEA and cortisol (taken as the independent variables) versus sAA (the dependent variable), again an association is found only upon awakening.