ATLANTA (AP) _ The federal Centers for Disease Control is sponsoring a program to randomly test the blood of up to one-third of the babies born in the United States next year for antibodies to the AIDS virus.

The tests will determine only whether the mother is infected. A positive result does not necessarily mean the child has or will get AIDS, said Dr. Timothy Dondero, head of the sero-epidemiology branch of the CDC's AIDS program.

Although the conclusions of several studies differ, they indicate that from 30 percent to 50 percent of the newborns testing positive could eventually get acquired immune deficiency syndrome, he said in an interview Tuesday.

Dondero said plans for the infant tests are in place so far in about 23 states plus Puerto Rico and the District of Columbia, and actual testing is under way in about half of those.

He said he expects participation of about 30 states by the end of the year and more in 1989. The study is part of a $40 million package of programs to track the spread of the AIDS virus.

The virus attacks the body's immune system, leaving victims susceptible to infections and cancer. The disease has claimed the lives of nearly 40,000 Americans.

AIDS is most commonly transmitted by sexual contact or by sharing contaminated drug needles. It is also spread, less often, from an infected mother to her child before or at birth.

It is likely that about 1.3 million infants will be tested next year, using a method first tried by Massachusetts health officials, Dondero said. No names will be attatched to the blood samples, he said.

''There is no way of testing specimens linked to individuals unless you have the consent of the individual,'' he said, adding that getting consent would hobble the random aspect of the sample.

''Most groups involved in testing - military recruits, sexually transmitted disease clinics, blood donors - are to some extent self-selected,'' he said. ''People do not agree to take part who have some reason for not wanting to take part.''

The new program is intended to test a true representative sample of the population, Dondero said. He said the aim is to determine where AIDS infection among women is concentrated and to determine where to target prevention programs.

''So far it is concentrated in big cities. It is important to assess if it is prevalent in some rural areas as well,'' he said.

''Over time we will be able to monitor trends of infection in the female half of the general population,'' he said.