Heat shock or stress proteins and glucocorticoids (cortisol) regulate a sequential pro-inflammatory and anti-inflammatory cytokine expression profile to effectively kill pathogens, whilst minimizing damage to the host. Cortisol elicits its effects through the glucocorticoid receptor (GR) for which Hsp70 and Hsp90 are required as chaperones. In common carp, (Cyprinus carpio) duplicated glucocorticoid receptor genes and splice variants with different cortisol sensitivities exist. We investigated the expression profiles of heat shock proteins Hsp70, Hsc70, Hsp90alpha and Hsp90beta and the three different variants of GR in vitro in and in vivo to define their role in immune modulation. A rapid transient induction of GR1 (a and b) and Hsp70 was seen after LPS treatment in vitro in head kidney phagocytes, whereas cortisol treatment did not affect constitutive or LPS-induced expression of Hsp70 or GR1 expression. In vivo zymosan-induced peritonitis upregulated GR and Hsp70 expression which appears to increase sensitivity for cortisol-induced immune modulation. Indeed, the increased GR and Hsp70 expression correlates with inhibition of both LPS- and zymosan-induced expression of pro-inflammatory cytokines. Infection with the blood parasite T. borreli decreases GR1a expression in thymus, but increases GR2 expression in spleen. Differentially regulated expression of Hsp70 and of glucocorticoid receptor variants with different cortisol sensitivities, underlines their physiological importance in a balanced immune response.