Taking birth control pills during early pregnancy doesn't appear to increase the risk of birth defects.
While some research has suggested a link between the use of birth control pills near conception and an increased risk of low birth weight, preterm birth or congenital urinary tract abnormalities, these concerns generally haven't been observed in clinical experience.
Birth control pills overall lower the risk of pregnancy and the risk of a fertilized egg implanting outside the uterus (ectopic pregnancy), which most often occurs in one of the tubes that carry eggs from the ovaries to the uterus (fallopian tubes). However, if you do conceive while taking a progestin-only birth control (minipill), there's a slightly higher chance that the pregnancy will be ectopic.
As a precaution, if you suspect you're pregnant, take a home pregnancy test. If the home pregnancy test is positive, stop taking the pill. If taking a home pregnancy test isn't possible, stop taking the birth control pill until the pregnancy is confirmed or ruled out. In the meantime, use another method of birth control — such as condoms.
If you're concerned because you took birth control pills before you knew you were pregnant, talk to your health care provider, but be assured that there's little risk.