The UN says it needs to reach all children up to the age of five and special measures would be taken to ensure children who were internally displaced by fighting were vaccinated.
Afghanistan's warring sides have agreed to a three-day ceasefire starting on Tuesday to enable the United Nations to immunize children against polio.
The UN said both the Taleban authorities and the opposing northern alliance had given their commitment to respect a ceasefire while the immunization programme takes place.
During the last polio vaccination programme in May and June this year, a similar ceasefire was respected by both sides.
Polio burden
The UN has set itself a daunting task in Afghanistan - the volunteers aim to vaccinate more than five million children during two rounds of national immunization days.
The UN says it needs to reach all children up to the age of five and special measures would be taken to ensure children who were internally displaced by fighting were vaccinated.
It said those crossing borders would also require special attention and the programme is taking place in Pakistan on the same dates.
The programme has been particularly successful in Pakistan, where the number of polio cases has dropped dramatically.
The UN said polio placed a burden on the Afghan population in terms of suffering, lost productivity and the increased need for medical resources.
The UN said they would carry out a further programme in November.