At enrollment, children’s height and weight were measured, axillary temperature was digitally recorded, and finger-prick blood samples were obtained to prepare thin and thick blood films and to determine hemoglobin concentration (Hb). Children known or suspected to be homozygous for sickle cell trait or pregnant were excluded. Any child found with a hemoglobin concentration <80g/L was referred by the nurse to the nearest health facility for iron therapy, and any child found with Hb <50g/L was taken to the hospital for transfusion. Baseline parasitaemia was measured in the intervention group during the first round of screening but was not measured in the control group owing to the ethical constraints of testing for malaria but not treating children found to be infected in the control schools, which was of particular importance at baseline as the intervention involved screening of _Plasmodium_ infection.

A questionnaire was administered to parents/guardians to record information on residence, family size, ownership of possessions, mosquito net use by them and their children, recent deworming of the child, house construction and parental education level.

# **_Intervention_**

IST was outlined as a possible strategy in the “ _Malaria-Free Schools Initiative_ ”, as part of the Kenya National Malaria Strategy 2009-2017 [38]. During IST, children were screened once a school term for malaria parasitaemia using an RDT (ParaCheck- _Pf_ device, Orchid Biomedical Systems, Goa, India) which is able to detect _P. falciparum._ Screening was conducted by laboratory technicians. Repeat visits were made to follow-up children absent on the day of screening. Children (with or without malaria symptoms) found to be RDT-positive were treated with a six dose regimen of artemether-lumefantrine (AL) (artemether 20 mg/lumefantrine 120 mg, Coartem®, Novartis) over three days. Doses of AL were based on weight, with children stratified into one of the four categories (<15 kg, 15-24.9 kg, 25-34.9 kg, and ≥35 kg). AL was given at a dose of 20/120 mg to children <15 kg, 40/240 mg to children 15-24.9 kg, 60/360 mg to children 25-34.9 kg, and 80/480 mg to those who weighed ≥35 kg. Parents or older siblings of children were called and a nurse explained that their child was infected with malaria parasites and required treatment. Doses 1, 3 and 5 were given under direct observation at the school by the study nurses. Children were given milk and biscuits with the AL and observed for 30 minutes after drug administration. If vomiting occurred during this period, drugs were re-administered. If vomiting occurred on a second occasion, this was noted but the drugs were not given again. Such children were not excluded from the trial and they were eligible to receive drugs on the subsequent two days. The parents/older siblings or study children themselves if in the older classes were given doses 2, 4 and 6 each day for evening administration and provided with instructions on treatment. Children absent from school on days two or three of treatment were followed up at their home by the nurse, and provided with the doses. Supervised treatment was defined as nurses administering and directly observing doses 1, 3 and 5 taken on three consecutive mornings in the school and recording doses 2 and 4 reported by the child as having been taken the previous evenings. No direct confirmation of whether dose 6 was taken was recorded by the nurse. The record of supervised treatment was used as a proxy for compliance. Five rounds of screening and treatment were implemented. The first round was conducted alongside baseline health assessments in March 2010, the second round in July 2010, the third in September 2010, the fourth in March 2011 and the final round in October 2011.

6