This study examined the effects that engagement in prayer had on the prayer agent. Psychophysiological measures were recorded during a study of affirmative prayer among lay members of Unity churches. The objects of the prayer were differentiated into two categories, either praying for self or praying for others, and were compared to a neutral activity of viewing photographs. Statistically significant improvements in heart rhythm coherence were observed when participants were engaged in prayer than when engaged in the neutral activity. Findings evaluating positive affect across the prayer and neutral activities were non significant and may be due to sample size. A negative correlation was found between the weekly amount of time spent in prayer and the coherence score while praying for others; praying for self was not significantly related to weekly prayer amount. No significant relationship emerged between perceived stress and the weekly amount of time spent in prayer. The study demonstrated the ability of affirmative prayer to alter heart rhythm patterns and to generate a state of psychophysiological coherence in the participants.