An etrog that was pierced and is missing a piece (ḥaser, deficient) is invalid for use on the first Yom Tov, as the etrog used then must be whole, as it is written: “On the first day you shall take (u-lekaḥtem)” (Vayikra 23:40). Our Sages expound: “lekaḥtem” means “lekiḥa tama” – something whole must be taken. However, during the rest of the festival, even if part of the etrog is missing, it is kosher. Even on the first Yom Tov, if the etrog was damaged by a thorn, and it is uncertain whether the etrog is missing a part, the etrog is kosher. Additionally, even if it is clear that the etrog was missing a piece, but it continued to grow and the site of the damage scabbed over, the etrog is kosher for the first Yom Tov (SA 648:2; Harḥavot 4:11:1-4).
If a ḥazazit – a sort of festering lesion – is found on the etrog and cannot be peeled off without removing some of the etrog’s flesh, then if the ḥazazit covers most of the etrog, it is invalid. Similarly, if a ḥazazit was found in two or three places that are spread out over most of the etrog, even if the ḥazazit, in the aggregate, does not cover most of the etrog, the etrog is invalid since it looks spotted. If the ḥazazit appears on the nose – the sloping upper part – of the etrog, even if it is small, if it stands out to a cursory glance, the etrog is invalid. A black, white, or strange-colored stain has the same status as a ḥazazit (SA 648:9-13, 16). These lesions and stains are very rare, as only anomalies invalidate the four species.
Common yellow, gray, and brown stains (bletlekh) do not invalidate the etrog, as they are normal for etrogim. These stains are generally caused by the etrog’s contact with leaves and branches, which lightly scratch it. The scratch causes the discharge of a liquid that forms a crust on the outside of the etrog. If these stains protrude and cannot be removed without taking off some of the flesh of the etrog, some people avoid using this etrog except in pressing circumstances (MB 648:50, 53). However, in practice, even if the stains protrude and cannot be scraped off, they do not invalidate the etrog, since they are commonly found on etrogim. Nevertheless, the more stains an etrog has, the less beautiful and mehudar it is.
It should be noted that after an etrog is picked, if it absorbs a light blow, there is concern that it will be damaged and discharge some clear liquid that will form a brown stain on the site. Though this stain does not invalidate the etrog, it does impair its beauty. For this reason, people generally wrap their etrog in flax or styrofoam mesh. If an etrog absorbs a blow, the discharged liquid should be rinsed off so that no stain forms.