How many chickens should a pregnant woman use for Kaparos:[1]

For a pregnant woman one is to take and slaughter one female chicken on her behalf, and one female and male chicken on behalf of the fetus whose gender is in question. [Thus, in total, a pregnant woman takes three chickens, two females and one male.]

How many chickens is a woman to take if she is pregnant with twins?[2]

It requires further analyses whether she is to suffice with three chickens as any pregnant woman or is to take five chickens.[3] Some Poskim[4] however conclude that she is to take 5 chickens.

If a woman gave birth after Kaparos but before Yom Kippur, should Kaparos be redone on the baby?

This matter requires further analyses.[5] However, some Poskim[6] conclude that she is not required to repeat the Kaparos on the infant.

If an ultrasound revealed the gender of the fetus, how many chickens are to be used?

Some Poskim[7] rule that one may follow the ultrasound and use a chicken of the projected gender. Others[8] rule that one should not rely on it.

Must a pregnant woman prior to 40 days of conception use 3 chickens?[9]

No.

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[1] Siddur Admur; Second custom in Admur 605:3; Poskim ibid in previous footnotes

Ruling of Admur in Shulchan Aruch 605:3: In the Shulchan Aruch 605:3 Admur records a difference in custom and rules as follows: According to the first custom [brought in previous footnotes] that allows exempting many males with one chicken and many females with one chicken, one is only required to take for a pregnant woman two chickens, one male and one female chicken. [Admur ibid; Rama 605:1; M”A 605:2; Mahril] The reason for this is because if the fetus is a male, then he has one male chicken as required, and if it is a female, then it suffices for the mother and fetus to have one female chicken. [Admur ibid; M”A ibid] However according to the second custom mentioned to take a chicken for each family member, a male for a boy, female for a girl, then one is to take for a pregnant woman three chickens, two females and one male. [Admur ibid] 

[2] See Likkutei Sichos 22 p. 59; Shaareiy Halacha Uminhag 2:250

[3] The question is that perhaps since this matter is uncommon, and it is in general a doubt whether one needs one chicken per person, then it is not required to take an extra two chickens for the twin.

[4] Kaneh Bosem 2:20

[5] See Hiskashrus 948 footnote 17 that perhaps the atonement for a pregnant woman is not for the fetus but for the woman, and hence once the child is born he needs his own atonement.

[6] Shevet Hakehasi 2:199; Piskeiy Teshuvos 605:2

[7] Kaneh Bosem 2:20

[8] Minchas Yitzchak in a gloss on the above Teshuvah of Kaneh Bosem

[9] Rav Wozner in Koveitz Mibeis Levi 2:17; Piskeiy Teshuvos 605:2