Her trip, the earliest by a secretary of state to Africa by any administration, will also see her hold talks with Sharif Sheikh Ahmed, president of Somalia's interim government.
"We think that the problems in southern Somalia have started to bleed regionally and internationally," Johnnie Carson, the most senior US diplomat for Africa, said last week.
He said violence in Somalia, which has not had a functioning central authority since 1991, has led to an exodus of refugees that has strained the capacity of its neighbours, especially Kenya.
Clinton will visit South Africa, Angola, the Democratic Republic of Congo, Nigeria, Liberia and Cape Verde.
Her trip follows a stop in Ghana last month by Obama, whose father was born in Kenya, where he appealed to Africans to hold their governments accountable
and fight corruption.
A Gallup poll released on Monday found that Obama's African roots have led to a jump in the popularity of the United States in sub-Saharan Africa, where 87 per cent of those surveyed in seven countries backed US leadership.