Under plans being finalised at the White House, Mr Clinton will convene a ceremony - probably in the small eastern Alabama town of Tuskegee, where the study began in 1932 - in which he will formally acknowledge official wrongdoing in an affair which fuelled black distrust of white government.
More than 600 people were recruited for the experiment, mostly impoverished rural blacks attracted in the depression era by promises of free food and medicine. Of them, 399 were infected with syphilis, but were not told they had the disease and were treated with placebos. The aim was to discover how untreated syphilis developed and killed people.
To that end black victims, the majority of whom died, were turned into human laboratory fodder. The experiment continued for a quarter of a century after penicillin was proved to be an effective cure for syphilis. Today, the survivors number just eight, aged between 87 and 106. Six of them had syphilis, while two were members of a control group who were not infected.
Since 1972, when the project came to light, the federal government has paid $10m (pounds 6.2m) in compensation to victims and their heirs. But no apology has been forthcoming. "The President feels we have a moral obligation," a White House spokesman said.
Attention to Tuskegee has grown since 1995 when Mr Clinton issued a formal apology for the equally unwitting guinea pigs of government radiation experiments during the Cold War.
Next week he will take part in ceremonies at a New York stadium honouring Jackie Robinson, who broke baseball's colour barrier 50 years ago. Mr Clinton is also considering other initiatives, including a White House conference on race.