Cancer of the cervix can now be prevented by vaccination against human papilloma virus. Demonstration projects have been successful but there are few reports of the challenges related to national school based programs. In conjunction with the Ministry of Health we conducted interviews and a household survey in three contrasting areas of Peru to obtain the perspective of different key actors. Of grade eligible girls 66% had received at least one dose, but 14% had discontinued. The main challenges were logistic: ensuring that that all schools participate; calculating the number of eligible girls; fitting the 3 doses into a 9m school year; written parental consent; coordination with schools; arrangements for a mopping-up strategy; combating discontinuation; reaching the distant and sparsely populated areas; and the additional work burden for health personnel. A lack of media information and educational materials left parents ill-informed but vaccine refusal was unusual. A two dose strategy will reduce the work load and cost but will not solve all the logistics problems. Ensuring an early start to the campaign based on estimated needs; a communication strategy to increase girls and parental motivation and community involvement are likely to increase coverage. Taking advantage of existing parent school interactions and considering "optout"would facilitate the consent process and, if acceptable, should be considered.