Children with Autism Spectrum Disorder (ASD) also often suffer from elevated stress and anxiety. These states can be measured via reports of behaviour (from self or others) or from physiological measures of stress, including the symptoms of Generalised Anxiety Disorder (GAD) and salivary cortisol, respectively. The use of these measures assumes a degree of reliability over time so that data from a specific period may be generalised to other periods. To measure the test-retest reliability of salivary cortisol and self-ratings of GAD in 27 high-functioning boys with ASD (M age = 12.1 yr., SD = 2.8 yr), samples were collected a mean of 2.4 yr. (SD = 0.5 yr) apart and analysed to test for the presence of a significant correlation within each variable over time. Results indicated that, although the concentrations of salivary cortisol increased over the period of the study, there was a significant correlation between the two measures of cortisol. GAD scores also showed a significant correlation over the period of the study. These findings suggest that both GAD and salivary cortisol data collected from boys with ASD may be reasonably inferred to represent fairly stable phenomena over time in research and clinical settings.