OBJECTIVE: To estimate the effect of improving waste collection services on waste disposal behaviour and exposure to environmental risk factors in urban, low-income communities in Pakistan. METHODS: We enrolled six low-income communities in Islamabad (Pakistan), four of which received an intervention consisting of a door-to-door low-cost waste collection service with centralised waste processing and recycling sites. Intervention communities underwent community-level and household-level mobilisation. The effect of the intervention on waste disposal behaviour, exposure to waste and synanthropic fly counts was measured using two cross-sectional surveys in 180 households per community. RESULTS: Intervention communities had less favourable socio-economic indicators and poorer access to waste disposal services at baseline than control communities. Use of any waste collection service increased from 5% to 49% in the intervention communities (difference 44%, 95% CI 41%, 48%), but the increase was largely confined to two communities where post-intervention coverage exceeded 80% and 90%, respectively. An increase in the use of waste collection services was also found in the two control communities (from 21% to 67%, difference 47%, 95% CI 41%, 53%). Fly counts decreased by about 60% in the intervention communities (rate ratio 0.4, 95% CI 0.3, 0.4) but not in the control communities (rate ratio 1.52, 95% CI 1.1, 2.2). The decrease in fly counts was largely confined to the two high-coverage intervention communities. CONCLUSION: Introduction of a low-cost waste collection service has the potential for high uptake in low-income communities and for decreasing the exposure to waste and synanthropic flies at household level. Intervention success was constrained by low uptake in half of the intervention communities.