Differential effects of noise exposure between substrains of CBA mice

•Circadian mechanisms are found to contribute to the vulnerability to noise trauma in mice.•Substrains of CBA mice differ in their circadian susceptibility to noise trauma.•CBA/Sca mice exposed to 103 dB SPL display differential day/night noise sensitivity but not CBA/CaJ or CBA/JRj mice.•Corticostereone levels were higher in Sca mice and peaked 4 h earlier compared to CaJ and JRj mice.•Differential vulnerability to noise trauma between inactive and active phase is not universal and might be governed by circulating corticosterone profiles.