The central nervous system is exposed to the chronic oxidative stress during aging when the endogenous defence weakens and the load of reactive oxygen species enhances. Sex hormones and heat shock proteins (Hsps) participate in these responses to stress. Their regulation is disturbed in aging. We assessed the expression of Hsps in hippocampus and cortex of follitropin receptor knockout (FORKO) mice, known to exhibit gender and age-dependent imbalance in sex steroids and gonadotropins. These imbalances could contribute to an impaired regulation of Hsps thereby increasing the risk of developing neurodegenerative disorders. Our study shows that, in the hippocampus the expression of Hsp70 and Hsp25 was reduced in 20-month-old FORKO mice. However, in the cortex both Hsps were significantly down regulated only in elderly females. There is a well-established co-regulation between Hsps and mitogen-activated protein kinases (MAPKs). Significant, gender-specific impairments in the translocation of phosphorylated ERK and JNK were found in the CNS structures in aged FORKO mice. Our results suggest that hormonal imbalances lead to a disturbed subcellular distribution of activated MAPKs which contribute to the impairments of signal transduction networks maintaining normal physiological functions in the cortex and hippocampus that are associated with neurodegenerative changes in aging.