We do not include “encompassing” directives in the count. E.g. “And keep My covenant” (Exodus 12:5), or “Concerning all that I have said to you, you shall beware…” (ibid. 22:30), or “And you shall be a holy people to Me” (ibid. 23:23).
We are not counting Psukim that don’t instruct us regarding a specific action, but regarding the imperative to observe all of the Torah’s commandments, are not included in the 613
The reason for a mitzvah is not counted on its own.
At times, the Torah tells us the reason for a command in language that could be understood as an independent precept—when in fact it is simply the rationale behind the words that precede it.
For example, “He shall not leave the Sanctuary, and he shall not desecrate the holy things of his G‑d” (Leviticus 21:12). Not desecrating the holy is not a commandment on its own, rather it is the reason why the Kohen may not leave the sanctuary. Or, “Her first husband, who had sent her away, may not take her again to be his wife…and you shall not bring sin to the land” (Deuteronomy 24:4). Here, too, “bringing sin to the land” is not an independent prohibition, but the reason why one may not remarry his divorced wife if she has remarried in the interim
A mitzvah that has both negative and positive components is counted as two—one Positive Commandment and one Negative Commandment.
E.g. we are commanded to rest on Shabbat and desist from work on the Shabbat. We are commanded to “afflict” ourselves on Yom Kippur and we are commanded not to eat on this holy day. Though a transgression of one is also a transgression of the other – if you eat on Yom Kippur you have not afflicted yourself; if you work on Shabbat you have not rested – nevertheless these are considered two independent mitzvot.
The different applications of a mitzvah are not individually counted.
E.g. one who inadvertently defiles the Temple or holy foods is required to bring a sin offering (Leviticus 5). If his financial situation allows, he is to bring a sheep or she-goat; otherwise he brings two birds; and if he is completely impoverished, he brings a flour offering. All this, however, is counted as one mitzvah—the mitzvah of bringing a sin offering when this particular offense is committed—although the execution of the mitzvah varies depending on the situation.
לא vs. לא
Do not count a negative statement amongst the prohibitions.
The Hebrew word “lo” can mean both “do not” and “shall not”; and only the “do not”s are counted as prohibitions. The only way to discern between the two is by studying the context of the word.
Examples: “She shall not go free as the slaves go free” (Exodus 21:7). This verse should not be construes as a prohibition, it is simply telling us that the circumstances that mandate the emancipation of a Canaanite slave do not apply to a Hebrew maidservant. Certainly, however, if the owner wishes to free her, he may do so.
Or, “So he shall not to be like Korach and his company” (Numbers 17:5). This is not a prohibition, rather a warning that anyone who dares contest the priesthood of Aaron’s descendents will meet the same fate as Korach and his cohorts.
Do not count the number of times a commandment is mentioned in the Torah, only the act which is prohibited or commanded.
Certain commandments are repeated in the Torah numerous times. For example, the commandment to rest on Shabbat is mentioned twelve times and the prohibition against consuming blood is repeated no less than seven times. Nevertheless, when counting the 613 mitzvot, we only count a prohibited or prescribed act once.
(The exception to this rule is those instances where the Sages have deduced that the repetition of a particular commandment is intended to prohibit or instruct us regarding a different act. In such a case, the [seemingly] repetitive verse is counted as a separate mitzvah—for it is in fact instructing us regarding something different than the first verse.)
It should be noted that though we count the prohibited acts, and not the amount of times mentioned, we only count prohibited acts individually specified in the Torah. At times, the Torah will issue a prohibition employing general terminology, for this prohibition includes multiple acts. For example, “You shall not eat over the blood” (Leviticus 19:26). This prohibition teaches us not to eat sacrificial flesh before the blood is sprinkled on the altar, not to eat from any animal before its soul (contained in its blood) has fully departed, that the members of a court may not eat on the day that they implement a capital verdict, and more. Though all these are biblically forbidden, none are counted as part of the 613—as none of them are mentioned specifically in the Torah.