Missouri is one of 28 states with this type of law.
The cost of the meningitis vaccine is $75 at the health department.
"I don't think anyone can get it for much cheaper in the private sector," said Conn Roden, director.
Bacterial meningitis is a rare infection of the brain and spinal cord. About 3,000 cases are reported each year, with 55 cases reported last year in Missouri.
Dr. Andrew Zupan, a pediatrician with Mercy Women and Children's Health Services, said that one-fifth of the 3,000 people who contract the disease (about 600) are college-age. This number is up from 300,10 years ago.
"The numbers are climbing," Dr. Zupan said.
Ten percent of those infected will die, according to the Centers for Disease Control and Prevention, and up to 20 percent of survivors will suffer brain damage, hearing loss, or limb amputations.
All students who will be living in student housing at the University Missouri-Columbia will receive information about the law and its implications in the mail.
Students will not be able to register for classes unless they get the vaccination or sign the waiver.
The University of Missouri-Columbia is offering the meningitis vaccine at orientation sessions for new students for $70.
Private colleges, such as Washington University, are not required to follow the new law, but officials say they will attempt to do so.
Bacterial meningitis is spread by coughing, sneezing, kissing, sharing glasses, utensils, and cigarettes.
The symptoms can easily be mistaken for the flu or a migraine. A rash and fever may also occur.
Zupan noted that smoking and smoke exposure are risk factors because smoke decreases the ability for the nose to fight bacteria that enters the body.
Another risk factor is living in close quarters, such as college students living in dormitories or with roommates, according to the CDC.
"The incidence of meningococcal disease in adolescents and college-aged young adults appears to have increased recently. College students in dormitories seemed to be the population with an increased risk," according to Dr. Thomas A. Hoffman, M.D., a professor at the University of Miami, whose report can be read at www.emedicine.com.
The meningococcal vaccine prevents on of the two most common bacterial forms of meningitis, Neisseria meningitidis. It lasts for three to five years and immunity fades with time.
However, because the vaccine does not cover all strains of Neisseria, it is only 60 percent effective, Dr. Zupan said.
Dr. Zupan said the cost of the vaccine varies from place to place. He suggests that people check with their insurance company and doctor's office for prices and availability.