The laws concerning the Red Heifer have always been regarded as the most mysterious of the Torah's Mitzvot. Although this Mitzva has always been considered to be above human reason, attempts have nevertheless been made to interpret it.

The Midrash states that the reason why a heifer is chosen is that it should atone for Israel's sin in worshipping the golden calf. Let the mother cow clean up the mess of her child. Its red color indicates blood guilt, as does the scarlet which was to be thrown into the midst of the burning animal. The heifer had to be one that had never borne a yoke since its purpose was to rid man of the yoke of sin. The cedar-wood which the Kohen took stands for pride, the hyssop for excessive humility. Both were thrown into water mixed with earth, giving an intermediate substance between solid and liquid to show that both extremes are undesirable. That the ashes of the heifer cleansed those who were unclean but defiled those who prepared and handled them is explained by the fact that what heals the sick may be dangerous for the healthy; what purifies the sinner is defiling to those without that sin. The use of ashes is to teach us that we, too, consist of dust and ashes; spiritual purification can never be attained where humility is lacking.

The person who had become defiled through contact with the dead was to be purified with the ashes of the heifer on the third and the seventh day following his defilement. The third day represents the third decade of a person's life when passions are at their height and sins have to be atoned for. The seventh day represents the seventh decade of human life when one should cleanse himself from sin before meeting his Maker. Symbolic explanations such as these do not fully explain the irrational nature of the Red Heifer.

The Talmudic view of the Mitzva of the Red Heifer is that it cannot be grasped by the limited human mind; G-d's will is beyond a human being's understanding. The Talmud tells of Rabbi Yochanan ben Zacchai who, having given a heathen an explanation of the Red Heifer from the world of witchcraft, when challenged by his disciples, said "The dead do not defile, nor do the waters purify: it is a Divine decree which we are not permitted to criticize." The rabbis noted that the word "chok", used in connection with the command of the Red Heifer, refers to a Mitzva the reason for which eludes human intellect. And it is with reference to this commandment that King Solomon, the wisest of men, exclaimed: "I said: I will get wisdom; but it was far from me" (Ecclesiastes 7:23)