Background The health of school-aged children (SAC) is often compromised by malaria parasitaemia (MP), soil-transmitted helminths (STH), and malnutrition in the tropics. The aim of this study was to determine the prevalence and influence of MP, STH and malnutrition on haemoglobin (Hb) levels as well as identify its predictors. Methods This cross-sectional study was carried out in SAC (4-14 years) in Owe, Mpundu and Meanja villages in Muyuka, Southwest Cameroon. Hb concentration was measured using a URIT-12 Hb meter while MP and STH were determined by Giemsa staining of blood films and Kato-Katz technique respectively. Anthropometric measures (weight, height and mid upper arm circumference (MUAC)) of malnutrition (z-scores of <−2 standard deviations below mean) were obtained by standard methods. Categorical and continuous variables were compared appropriately, and multiple linear regression model was used to determine predictors of Hb level. Results The prevalence of MP, STH, anaemia and malnutrition in the 401 SAC examined were 33.9%, 2.2%, 75.3% and 24.4% respectively. The prevalence of MP varied significantly with locality (P = 0.031). Stunting occurred commonly (23.7%) and was significantly higher in males (28.6%), children 11-14 years old (38.3%) and those of Meanja locality (47.4%) than their counterparts. Significantly higher prevalence of anaemia was observed in children of Meanja (89.5%) and those both MP positive and malnourished (86.2%). Moderate anaemia occurred commonly (60.6%) and children �6 years old had significantly (P = 0.034) higher