Here's the section from Emily Oster's book Expecting Better on Vitamin K shots. I highly recommend the book if you haven't already read it. She does a great job examining the many pregnancy "no-no"s and questions you might be dealing with to help you make your own decisions. I know it's been a life-saver for me during my pregnancy so far.
Vitamin K Shots
It is standard to give babies vitamin K supplementation within the first hours after birth. The purpose is to prevent bleeding disorders. A deficiency of vitamin K can cause unexpected bleeding in up to 1.5 percent of babies in the first week of life (the bleeding could come from the umbilical area, be prompted by a needle stick, or be internal). It can also cause bleeding later, between 2 and 12 weeks of age. Although it’s rare (perhaps 1 in 10,000 babies ), this second manifestation is much worse: it often causes severe neurological damage or death.
Supplementation with vitamin K is very good at preventing this. It’s typically given through a shot, although it can also be given orally. Evidence suggests that both are effective, but the oral dosing slightly less so. 3 Vitamin K supplementation has been standard since the 1960s. Unless you ask about it, you probably will not even know the doctor is doing it; it’ll just be one of the several things they do when they are cleaning up the baby.
Despite the fact that it’s standard, this shot is not free of controversy. In the early 1990s, several studies from the United Kingdom suggested that these shots might be linked to an increased risk of childhood cancer. In one study, researchers compared 33 children who developed cancer before age ten to 99 children who did not. They looked at many factors and found that vitamin K shots were one thing that was more common among the children with cancer. 4
The same researchers followed up with a slightly larger study (195 children with cancer) and again found that vitamin K shots were more common among the children with cancer than those who were not sick. 5 The authors argued that, in particular, vitamin K shots were associated with cancer, while vitamin K given orally seemed to make no difference.
Although this may give you pause, further work has not provided support for this claim. For one thing, other researchers pointed out that because childhood cancer is, mercifully, rare, if there was any connection between vitamin K and cancer, we would expect to see huge increases in childhood cancers after these shots became standard in the 1960s, and we do not. 6 Further, attempts to replicate the study by other researchers have not shown similar results. 7
The American Academy of Pediatrics responded to this controversy in 2003 with a review of the debate and reaffirmed their position that vitamin K shots should be standard. They argued that the benefits in preventing bleeding were large, and the best available work suggested no link with cancer. 8 This seems correct to me. Although the specter of childhood cancer is scary, the evidence is simply not there to support a link to vitamin K supplementation, and we know for sure that bleeding disorders are a risk.
Oster, Emily (2013-08-20). Expecting Better: Why the Conventional Pregnancy Wisdom Is Wrong-and What YouReally Need to Know (pp. 258-259). Penguin Group US. Kindle Edition.