Background <p>Cluster headache is associated with compensated hypogonadism in males, suggesting impaired testicular steroidogenesis. It is unknown if adrenal steroidogenesis is dysregulated and how this is linked to cluster headache pathophysiology. We therefore aimed to define the adrenal steroid profile in cluster headache and define the differences between the phases of episodic cluster headache. We secondarily aimed to assess whether the steroid profile could distinguish between chronic cluster headache and episodic cluster headache.</p> Methods <p>A prospective case-control study containing adult males with chronic cluster headache (<i>n</i> = 60), paired episodic cluster headache in and out of bout (<i>n</i> = 60) and healthy controls (<i>n</i> = 60). A fasted serum steroid profile for 16 steroid hormones was assessed via liquid chromatography tandem mass-spectrometry, assessing mineralocorticoids, glucocorticoids, and androgens. Explorative machine learning was used to segregate the cluster headache states.</p> Results <p>The mineralocorticoids 11-deoxycorticosterone (<i>P</i> &lt; 0.05), corticosterone (<i>P</i> &lt; 0.05) and aldosterone (<i>P</i> &lt; 0.05) were lower in those with episodic cluster headache compared to controls. 11-deoxycorticosterone (<i>P</i> &lt; 0.01), corticosterone (<i>P</i> &lt; 0.01), and the glucocorticoids 11-deoxycortisol (<i>P</i> &lt; 0.01) and cortisol (<i>P</i> &lt; 0.05) and cortisol/DHEAS ratio (<i>P</i> &lt; 0.001) are lower in episodic in bout compared to their paired remission state. Those with chronic cluster headache had lower concentrations of 17-OH pregnenolone (<i>P</i> &lt; 0.05) and DHEAS (<i>P</i> &lt; 0.001) and a higher cortisol/DHEAS ratio (<i>P</i> &lt; 0.01). The steroid hormone profile distinguished between chronic and episodic cluster in bout with a specificity of 86% (95%CI: 69%-90%), sensitivity of 81% (95%CI: 73%-93%) and AUC of 0.92 (<i>P</i> &lt; 0.0001). Attack frequency and time from last attack correlated with the degree of steroid dysfunction in episodic cluster headache but not in chronic cluster headache.</p> Conclusion <p>We identify distinct steroid hormone profiles in episodic and chronic cluster headache. Episodic in bout was associated with reduced adrenal steroid synthesis that resolves in remission. Chronic cluster headache was associated with stress induced androgen suppression. Together, these differences are likely secondary to cluster headache and may reflect distinct neurobiological bases underlying episodic and chronic cluster headache.</p> Clinical trail number <p>Not applicable.</p> Graphical Abstract <p></p>