The question of punishments in natural law had already posed a problem to Thomasius in the Institutes of 1688, and it is at least in part the theoretical challenge associated with punishment that caused him to refine and modify his natural law theory after 1688. Laws, he had argued in the Institutes, were expressions of the will of a superior who punished all transgressions of his law. The problem in the case of natural law is that there are no evident divine punishments. Although acting contrary to natural law may sometimes prove a disadvantage, it is not invariably followed by an unmistakable sign of divine anger. A thief is not struck by lightning. And unless it is clear that the evil following from a transgression of natural law is a punishment inflicted by the superior, the punishment does not fulfill its purpose of signaling God's displeasure to his subjects. As Thomasius himself wrote, “if God does not care about the affairs of humans, there will be no ruler and, therefore, nobody to be obeyed.”

It could be argued that divine punishments were not inflicted immediately because they were reserved for the afterlife. Leibniz, for example, admitted that the transgressors of natural law had not always received their punishment in temporal life, but he insisted that humans were able to know on the basis of reason that God would punish them for their trespasses in the afterlife. “One cannot doubt,” Leibniz declared, in his “Opinion on the Principles of Pufendorf,” “that the ruler of the universe, at once most wise and most powerful, has allotted rewards for the good and punishments for the wicked, and that his plan will be put into effect in a future life, since in the present life many crimes remain without punishment and many good deeds without recompense.” For this it was necessary to assume that the existence of an afterlife and the immortality of the soul were truths of natural reason, like natural law itself.