The Kenyan authorities will include an intersex category, along with "male" and "female", in the section on gender in next month's census, an official from the statistics bureau has confirmed to the BBC.
It will form part of efforts to gather data on the number of intersex people in the country.
"Intersex" is an umbrella term that describes people who are born with a variety of characteristics that do not fit into traditional conceptions of female or male bodies.
The UN believes that up to 1.7 per cent of the world's population have intersex traits.
A special task force had been set up by the government to look into the interests of intersex persons and will identify reforms required to respect and protect their rights as Kenyans.
The census is expected to take place at the end of next month.