The recall is for the Haemophilus influenzae type B vaccine, commonly known as the Hib vaccine, which protects against invasive diseases, the Whitehouse Station, N.J., company said.
The recall affects 10 lots of Hib vaccine, and two lots of a combination vaccine for both Hib and hepatitis B, shipped after April, the U.S. Food and Drug Administration said.
Centers for Disease Control and Prevention Director Julie Gerberding told The Wall Street Journal the CDC saw no health threat if children received the recalled vaccine. At worst, a child might experience a skin irritation around the vaccination site, the CDC said.
There have been no reports of contamination, officials said.
The CDC said U.S. doctors administer about 14 million Hib doses annually and Merck makes about half the supply, so shortages could occur.
Paris's Sanofi Pasteur SA, a unit of drugmaker Sanofi-Aventis SA, is the other Hib vaccine provider.
Merck said it announced the recall after identifying a sterility problem in a West Point, Pa., factory.
It said concerned parents should contact their child's doctor.