Rural and remote Papua and West Papua are among the most important regions for Indonesia to achieve the second MDG on primary education with equity. Both provinces have gross, net enrolment and literacy rates which barely touch the national averages. Given the distinct political, socio-cultural, and geographical aspects of Papua and West Papua from the rest of the country, central government provides greater autonomy for local policies. In that light, Papua and West Papua have launched the Affirmative Education Policy Document which outlines key strategies to increase access and quality for indigenous Papuans and population in rural and remote areas. A fundamental concern about the quality of education, acknowledged in the policy document is the high rate of illiteracy among indigenous Papuans and population in rural and remote areas. A number of recent reports confirm the high illiteracy levels and reiterate the concern that illiteracy rates are not only high among rural and remote out-of-school school children and youth but also among children enrolled in primary schools. A number of factors have been identified as contributing to illiteracy rates and poor education attainment in basic education for children in Papua and West Papua. They include: low quality pre and in-service teacher trainings, acute teacher absenteeism, and infrequent and poor supervision of schools and teachers. An additional significant and challenging factor is the serious lack of teaching and learning materials that reflect indigenous Papuan realities or build on the local-context in the creation of primary school literacy programs. This last factor has been said to create an environment where children (new learners) feel alienated from the materials presented with low motivation to learn. Because the current literacy materials for the early grades are predominantly non indigenous and generically Indonesian many young indigenous Papuan children are becoming disengaged from early learning, dropping out or just moving through school classes but not mastering literacy (and numeracy skills) and never realizing their learning potential or their right to an education. More recent programmes generated through partnerships with different organization have recognized this significant gap in context appropriate materials and explored and implemented new models and approaches that show some potential for positive change.