BACKGROUND: Despite progress in improving health outcomes in Afghanistan by contracting public health services through non-governmental organizations (NGOs), inequity in access persists between the poor and non-poor. This study examined the distributive effect of different contracting types on primary health services provision between the poor and non-poor in rural Afghanistan. METHOD: Contracts to NGOs were made to deliver a common set of primary care services in each province, with the funding agencies determining contract terms. The contracting approaches could be classified into three contracting out types (CO-1, CO-2 and CO-3) and a contracting-in (CI) approach based on the contract terms, design and implementation. Exit interviews of patients attending randomly sampled primary health facilities were collected through systematic sampling across 28 provinces at two time points. The outcome, the odds that a client attending a health facility is poor, was modelled using logistic regression with a robust variance estimator, and the effect of contracting was estimated using the difference-in-difference approach combined with stratified analyses. RESULTS: The sample covered 5960 interviews from 306 health facilities in 2005 and 2008. The adjusted odds of a poor client attending a health facility over time increased significantly for facilities under CO-1 and CO-2, with odds ratio of 2.82 (1.49, 5.36) P-value 0.001 and 2.00 (1.33, 3.02) P-value 0.001, respectively. The odds ratios for those under CO-3 and CI were not statistically significantly different over time. When compared with the non-contracting facilities, the adjusted ratio of odds ratios of poor status among clients was significantly higher for only those under CO-1, ratio of 2.50 (1.32, 4.74) P-value 0.005. CONCLUSIONS: CO-1 arrangement which allows contractors to decide on how funds are allocated within a fixed lump sum with non-negotiable deliverables, and actively managed through an independent government agency, is effective in improving equity of health services provision.