all children in class 1 and 5 were requested to provide individual written informed consent and they were given the option to withdraw their child from the study at any time. Prior to every IST round or assessment the procedures were explained to the children and they were required to provide verbal assent. An independent data monitoring committee reviewed the trial protocol, data analysis plan and preliminary results.

# **_Study area and population_**

The trial was conducted from January 2010 to March 2012 in Kwale and Msambweni districts on the south Kenyan coast (Figure 1). Malaria transmission in the area is low to moderate and perennial with seasonal peaks following the two rainy seasons (April-July and September-November) [31]. The primary malaria vectors are _Anopheles gambiae s.l._ and _Anopheles funestus_ [32,33]. Intensity of malaria transmission has been declining in recent years: school surveys conducted in 2010 reported prevalences of _P. falciparum_ of 9-24% [34,35], compared to 64% in 1998 [32]. Overall reported net use in the region is high, with the communities having benefited from universal coverage campaigns. During the two-year trial period, albendazole was delivered through households as part of the National lymphatic filariasis campaign in 2011, although coverage was not extensive and Praziquantel was delivered schools in the area in June 2011. The vast majority of the population in these districts belong to the Mijikenda ethnic group, with Digo and Duruma the predominant subgroups [36]. The region is primarily rural with subsistence farming of maize and cassava practiced by many of the communities, although titanium mining has recently become an important source of employment. In economic and educational terms, the districts are ranked the seventh poorest in Kenya and consistently have some of the worst performing schools in the national school examinations [37].

Kwale District has 85 schools across four zones, and in two of these an alternative literacy intervention study was underway. Therefore only 20 schools from Mkongani and Shimba Hills zones were included in our study, allowing the two interventions to proceed without leakage. In Msambweni District 81 of the 112 schools were selected, with schools in Lunga Lunga and Mwereni zones greater than 70 km away from the project office excluded because of logistical considerations in visiting them.

# **_Study design_**

The study was designed as a factorial cluster randomized trial to investigate the impact of two interventions: (i) the impact of school-based IST of malaria on the health, sustained attention and education of school children, and (ii) the impact of a literacy intervention on education. In order to evaluate the potential interaction between the two interventions, schools were randomized to one of four groups, receiving either: (i) IST alone; (ii) the literacy intervention alone; (iii) both interventions combined; or (iv) control group where neither intervention was implemented (Figure 2). The study was not blinded. Due to the factorial design of the trial and lack of interaction detected (interaction effect p-values of 0.45, 0.26 and 0.60 for the three key literacy outcomes) between the two interventions in class 1 where both were implemented, we report the results of the interventions separately. Only the IST intervention results are reported in this paper. The results of the literacy intervention will be reported in a separate paper 4