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BACKGROUND: Insomnia is common among patients with stable heart failure (HF) and associated with inflammation and altered autonomic function. PURPOSE: The purposes of this study were to examine the effects of cognitive behavioral therapy for insomnia (CBT-I) on the Hypothalamic Pituitary (HPA) Axis, autonomic function, inflammation and circadian rhythmicity and the associations between these biomarkers and insomnia, sleep characteristics, symptoms, functional performance, and sleep-related cognitions. METHODS: We conducted a sub-analysis of a pilot randomized controlled trial (RCT) (NCT02827799) whose primary aim was to test the effects of CBT-I on insomnia. We randomized 51 patients with stable Class II-IV HF to CBT-I (n = 30) or attention control (n = 21). Participants completed wrist actigraphy and self-reported insomnia severity, sleep characteristics, sleep-related cognitions, daytime symptoms, and functional performance. We measured day and nighttime urinary free cortisol, melatonin sulfate, epinephrine and norepinephrine at baseline and 2 weeks after CBT-I and computed general linear models and partial correlations. RESULTS: CBT-I had no effects on the biomarkers, but there were statistically significant negative cross-sectional correlations between the ratio of day/night urinary free cortisol and sleep disturbance, anxiety, fatigue, depression, and negative sleep cognitions. Increases in the ratio of day/night cortisol were associated with statistically significant improvements in fatigue, depression, sleep duration and sleep-related cognitions. CONCLUSIONS: Biomarkers of stress and autonomic function are associated with sleep, sleep-related symptoms and cognitions among people with chronic HF. Future studies are needed to identify potential causal relationships and the impact of sleep interventions.