Objective The aim of this study was to investigate relations (or coactions) among maternal mental health measures, clinical and socio-demographic factors and salivary cortisol level of hospitalized mothers and babies. Design A cross-sectional observational and exploratory study at a tertiary referral centre. Setting Maternal and Neonatal Care Ward of the University Hospital of Brasilia, Brazil Population 89 mother-baby dyads at post-delivery period. Methods Dyads were recruited by convenience during the first 48 hours after birth. Main outcome measures The research protocol included maternal sociodemographic and clinical data, screening for maternal depression, self-efficacy and gestational stress, besides salivary cortisol collection from both mother and baby. Results: Exploratory analysis indicated a relation between high gestational stress, high depression symptoms, low self-efficacy perception and high baby’s cortisol level (p < 0.05). Maternal cortisol was positively related to infant cortisol and was indirectly influenced by maternal perception of self-efficacy in reading the baby’s behavior, especially for knowing what the baby likes, or what pleases her/him, maternal situational beliefs (within the concept of parental self-efficacy). Four binary logistic regression models were performed considering maternal mental state variables as factors and clinical and socio-demographic variables as covariates in order to predict the cortisol level of infants. Only two were strong predictors, namely maternal depression and higher gestational stress. Conclusion The findings suggest an important role of maternal mental health in neonatal salivary cortisol levels in the first days of life, which can be considered an early clinical marker for the infant’s reaction to maternal mental status.