CpGs in hypothalamic–pituitary–adrenal HPA axis genes significantly correlated with cortisol levels in children whose mothers had prenatal post‐traumatic stress disorder (PTSD). (a) cg27193031 (r = 0.27, adj.p = 0.017), (b) cg25328597 (r = 0.2, adj.p = 0.034), (c) cg04672351 (r = 0.36, adj.p = 0.01), (d) cg10106856 (r = 0.24, adj.p = 0.009), (e) cg26868354 (r = 0.31, adj.p = 0.034), (f) cg14939152 (r = 0.26, adj.p = 0.033), (g) cg17349736 (r = −0.31, adj.p = 0.007), (h) cg23329208 (r = 0.33, adj.p = 0.019). CpGs first passed adjustment for multiple testing using Holm method p < 0.05. adj.p, p values after multivariate linear regression, adjusted for estimated blood cell proportions, child age and sex, maternal age, education, marital status, location and prenatal smoking status, and batch effects. CpGs shown are methylation measures which were significant in participant group with maternal PTSD. r = correlation coefficient in PTSD group. Y‐axis represents % methylation