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The non-cognitive effect of malaria in relation to school attendance among primary school pupils in Khana Local Government Area, Rivers State, Nigeria was assessed using a cross sectional survey approach. Two sets of self-structured questionnaires were produced and distributed among teachers and pupils of six randomly selected primary schools in the study area. All the 60 questionnaires distributed to 60 teachers in the 6 primary schools were answered and returned. Out of the 60 respondents, 21(35%) were males while 39 (65%) were females, 47(78.3%) were form teachers while 13(21.7%) were regular teachers. Among the form teachers, 78.3% (P<0.05) mark pupils' attendance register daily but all the teachers (100%) agreed that pupils have been absent from school on account of poor health, 60% agreed that an average of 1-5 pupils were absent from school per week on account of poor health while 75% (P<0.05) claimed that malaria was the commonest disease that caused pupils' absenteeism from school. Pupils that missed test/examination due to absenteeism were not considered for make-up test by 72% (P<0.05) of the teachers. Out of 120 pupils investigated, 87(72.5%) have been absent from school on account of ill health. Malaria caused 79(90.8%) of the pupils to be absent and during treatment, all the pupils kept away from school. 68(83.5%) were not able to meet up lost lessons and this affected the grade of 80% of the pupils. However, they were all promoted to the next class. Policy makers, health agencies and other stakeholders should consider appropriate control measures that will meliorate malaria-related school absenteeism in the study area. [ABSTRACT FROM AUTHOR]