The present study aimed to report the prevalence of anaemia and iron deficiency (ID) and to explore the associations among socio-demographic characteristics, nutritional status and inflammation status in the occurrence of anaemia and ID in a nationally representative sample of Malaysian primary schoolchildren. Using data from the South East Asian Nutrition Surveys (SEANUTS), 544 Malaysian children aged 7 to 12 years were included in this secondary analysis. Blood samples were drawn for haemoglobin and serum ferritin analysis while C-reactive protein (CRP) and α-1-acid glycoprotein (AGP) were measured to detect inflammation. Prevalence of anaemia and ID were 4.0% and 5.2%, respectively. There were significantly more anaemic indigenous bumiputra children (9.9%) than Chinese children (0.6%). Correction for inflammation did not change the prevalence of ID. More overweight/obese children than thin/normal weight children were found to have elevated acute phase protein (APP). Children with elevated inflammatory markers had significantly higher ferritin level than children without inflammation. Periodic health assessments of anaemia and ID at the population level to monitor and clarify the epidemiology of health problems are required to inform public health policies and strategies.