ABSTRACT: Aplasia of the septum transversum (AST) is a malformation that results in alterations in ventricle morphology. The condition has been linked to increased mortality during periods of increased cardiac demand in Atlantic salmon Salmo salar. The blood plasma biochemical response to an acute hypoxic event (1 h at 31-39% O₂ saturation) was investigated in fish with and without a septum transversum to assess levels of anaerobic respiration (lactate) and the stress response (cortisol, glucose, osmolality, Na⁺, Cl^- and K⁺). AST had no effect on body size parameters or relative ventricular mass. The hypoxic event increased the levels of anaerobic respiration and induced a typical stress response. Contrary to our expectations, AST had no effect on any plasma parameter in normoxia or following severe acute hypoxia. We conclude that in the current scenario, AST does not affect the levels of anaerobic respiration or the plasma stress response in Atlantic salmon.