After two decades of war and conflict in Afghanistan, the public-health system is in disarray and malaria has re-emerged as a major disease, with Plasmodium falciparum malaria becoming increasingly common. The limited healthcare services that are available are mainly delivered by non-governmental organizations in collaboration with the Ministry of Health. Although chloroquine (CQ) remains the official first-line treatment against P. falciparum malaria, there is little information on the severity or distribution of resistance to this drug in Afghanistan. In-vivo surveys, co-ordinated by the Malaria Reference Centre in Jalalabad, were therefore performed to determine the frequency and grades of CQ resistance in the three eastern provinces of Kunar, Nangarhar and Laghman. Of the 142 cases enrolled in the study, only 47 (33%) were sensitive. Most of the cases (55%) showed RI resistance but RII/RIII resistance was not uncommon (11%). The prevalence of resistance appeared similar in children and adults, in males and females, and in each of the three provinces investigated. Gametocyte carriage post-treatment was elevated in the resistant cases. As in neighbouring Pakistan, the resurgence of P. falciparum in Afghanistan is probably associated with the transmission and spread of chloroquine-resistant strains. The first-line therapy used against P. falciparum malaria must be changed in order to reverse this trend.