Islamic praying (Namaz) can be considered a mental, spiritual, and physical practice. The study aimed to investigate the early effect of Namaz on stress-related hormones and the expression of stress-induced genes such as IL6 and BDNF. Eighty-three healthy women and men who continually practice Namaz participated in the study. The saliva samples were taken before and after Namaz to measure cortisol and alpha-amylase hormone levels. Also, to evaluate the expression of BDNF and IL6 genes, 11 specimens were selected randomly. Based on baseline sampling, the participants were classified into three groups: cortisol levels lower than 5, between 5–15, and upper than 15 ng/ml. The results indicated that cortisol significantly increased and decreased in the first and third groups after Namaz, respectively. In addition, the increase of alpha-amylase also occurred in subjects with a low baseline level of its concentration. Regarding genetic expression examination, there was a significant decrease in BDNF gene expression after the Namaz. In addition, the change of cortisol and alpha-amylase hormones after Namaz related to the baseline level changed to approach the optimal range after Namaz. These findings were reported for the first time and need more studies.