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The paper employs techniques of multilevel modelling and geographical information systems (GIS) on Malawi’s SACMEQ1 I, II and III data to identify factors affecting pupil performance in primary education of Malawi. The study reveals that in some districts pupils performed much better than others. Whilst in majority of cases the achievement levels of pupils were closely associated with the levels of inputs and services, there were some districts that did not demonstrate a positive correlation. The analysis further shows that pupils’ low socioeconomic status, high pupil-teacher ratios and the more time head teachers spent in teaching other than on school management were more significant factors that negatively affected pupil performance.