BACKGROUND: Introducing sustainability and self-reliance is essential in chronic humanitarian emergencies before financial assistance is phased out. In Pakistan-based Afghan refugee camps, this was attempted through shifting from indoor residual spraying (IRS) to the subsidized sale of insecticide-treated nets (ITNs) for prevention of malaria and anthroponotic cutaneous leishmaniasis (ACL). Here we outline the strategy and document the progress to provide guidance for replication of similar approaches in other chronic refugee situations. METHODS: The operational monitoring data presented were collected through: (i) two surveys of knowledge, attitude and practice (KAP); (ii) routine sales reporting of health-care providers; (iii) records completed during field visits; and (iv) registers used during annual re-treatment campaigns. RESULTS: From 2000 until 2003, subsidized ITN sales expanded from 17 to 44 camps. Based on 2003 sales records, maximum coverage from subsidized sales exceeded 50% in 13 camps and 20% in an additional 14 camps. Free annual treatment campaigns showed that many refugees were in possession of non-programme nets, which were either locally-made or had leaked from an ITN programme in Afghanistan. Estimated re-treatment coverage of sold and existing nets through annual campaigns exceeded 43% in all camps and was above 70% in the majority. CONCLUSION: Subsidized sales of ITNs have effectively introduced the components of sustainability and self-reliance to the prevention of malaria and ACL in Afghan refugee camps. Similar approaches should be investigated in other chronic refugee situations to discourage expectations of continuing humanitarian donations that cannot be fulfilled.