Background: Anemia in children continues to be a major public health challenge in most developing countries. This study determined the prevalence of anaemia and its associated risk factors among children under five in four rural communities in the Hohoe Municipality. Methods: A descriptive community-based cross-sectional study was carried in November 2015. Interviews with semi-structured questionnaires were used to obtain information from mothers of children on socio-demographic characteristics, dietary and feeding practices of the children. Axillary temperature and anthropometric indices were measured using standard methods. Finger-prick blood samples were collected for Haemoglobin concentration measurement and blood film for malaria parasites. Chi-squared test and logistic regression were used to determine theassociation between dependent and independent variables. Results: Of the 235 children surveyed, 113 (48.1%) were anaemic (Hb<11.0g/dl) and17 (7.2%) had low Haemoglobin (Hb< 8.0g/dl). Malaria prevalence by microscopy was 40 (17.0%)andlong-lastinginsecticide-treatednet (LLIN) usage was 173 (73.6%). Anaemia was significantly higher among children aged 6-23 months than those aged 24-59 months (χ 2 =4.91, p=0.027).Children of mothers aged between 40-49 years were 84% times less likely to have anaemia as compared to those aged less than 30 years (AOR=0.16, p=0.005). Children who tested negative for malaria were 75% times less likely to have anaemia (AOR=0.25, p<0.001).No significant difference was observed between males and females, LLIN usage and consumption of iron, vitamin B12, folate and anaemia. Conclusion: Anaemia prevalence in the rural Hohoe Municipality is relatively low compared the 74% reported bythe Ghana Demographic Health Survey in 2014 for rural Ghana. Age of mother and malaria parasitaemia were factors found to be contributing significantly to anaemia. Future interventions should include promotion of foods containing iron, Vitamin B12 and folate, continuous use of LLIN and intermittent preventive treatment of asymptomatic malaria.