The Government of Kenya is interested in understanding how malaria prevention and treatment can improve the education of school children when it is combined with effective teaching. This project examines the impact of school-based malaria intermittent screening and treatment and enhanced literacy training and support for teachers on children's health and educational outcomes. A cluster randomized trial was implemented with 5,233 children in 101 government primary schools on the south coast of Kenya in 2010-2012. The intervention was delivered to children randomly selected from classes 1 and 5 who were followed up for 24 months. Once a school term, children were screened by public health workers using malaria rapid diagnostic tests (RDTs), and children (with or without malaria symptoms) found to be RDT-positive were treated with a six dose regimen of artemether-lumefantrine (AL). Given the nature of the intervention, the trial was not blinded. The primary outcomes were anemia and sustained attention. Secondary outcomes were malaria parasitaemia and educational achievement. Data were analyzed on an intention to treat basis. The study is registered with ClinicalTrials.gov, NCT00878007. The schools were randomly assigned to one of four experimental groups: some schools have been tested and treated for malaria; some schools have had extra support for teachers of English and Swahili; some schools have been both tested for malaria and received extra teacher support; and other schools have gotten neither of the two programs. Following recruitment, baseline health and education surveys were undertaken in January-February 2010, which were followed by the first round of intermittent screening and treatment (IST) and the teacher training workshop. Classroom observations occurred in May 2010, followed by the second round of IST in June-July 2010. The third round of IST occurred in September 2010. The first follow-up education surveys were carried out in November 2010 and the first health surveys in February and March 2011, followed by a round of IST as well as refresher teacher training for the literacy intervention. The final round of IST was conducted in September 2011 with the 24 months follow-up health and education survey in February-March 2012. The data from the baseline and follow-up surveys is documented here.