A controversial body of literature demonstrates associations of geomagnetic storms (GMS) with numerous cardiovascular, psychiatric and behavioural outcomes. Various melatonin hypotheses of GMS have suggested that temporal variation in the geomagnetic field (GMF) may be acting as an additional zeitgeber (a temporal synchronizer) for circadian rhythms, with GMS somehow interfering with the hypothesized system. The cryptochrome genes are known primarily as key components of the circadian pacemaker, ultimately involved in controlling the expression of the hormone melatonin. Cryptochrome is identified as a clear candidate for mediating the effect of GMS on humans, demonstrating the prior existence of several crucial pieces of evidence. A distinct scientific literature demonstrates the widespread use of geomagnetic information for navigation across a range of taxa. One mechanism of magnetoreception is thought to involve a light-dependent retinal molecular system mediated by cryptochrome, acting in a distinct functionality to its established role as a circadian oscillator. There is evidence suggesting that such a magnetosense--or at least the vestiges of it--may exist in humans. This paper argues that cryptochrome is not acting as secondary geomagnetic zeitgeber to influence melatonin synthesis. Instead, it is hypothesized that the cryptochrome compass system is mediating stress responses more broadly across the hypothalamic-pituitary-adrenal (HPA) axis (including alterations to circadian behaviour) in response to changes in the GMF. Two conceptual models are outlined for the existence of such responses--the first as a generalized migrational/dispersal strategy, the second as a stress response to unexpected signals to the magnetosense. It is therefore proposed that GMS lead to disorientation of hormonal systems in animals and humans, thus explaining the effects of GMS on human health and behaviour.