Background: Childhood anaemia is a severe public health problem in most sub-Saharan African countries including Tanzania. We assessed prevalence and risk factors for anaemia among children under the age of 5 years in Handeni District Tanga region Tanzania. Objective: To assess prevalence and risk factors for anaemia among children less than five years in Handeni district and document variability of haemoglobin by village and months. Methods: Cross-sectional survey study was conducted whereby data were collected every month in 30 rural villages of Handeni district. A total of 2,120 children were seen across 12 month period in 2007. Data on various social demographic and medical characteristics were collected and analysed. Children were regarded anaemic if they had Haemoglobin level <11g/dl and underweight if Weight-for-age Z-score was less than -2 Standard Deviation based on reference growth standards developed by the WHO. Data were analysed in two ways, one using anaemia as a binary outcome and the other using haemoglobin as a continuous outcome. Findings: Anaemia (Haemoglobin level <11.0 g/dl) was detected in 44% of the 2,120 children. Anaemia was associated with malaria (positive paracheck test), use of antimalarial drugs and underweight in children. Anaemia was more common in males (49%) compared to females (40%) χ2, =18, p-value <0.001 and more common among younger than older children (χ2, =114, p-value <0.001). Family socio economic status were not associated with anaemia (all levels p-value >0.05). A multivariable model for the child’s anaemia revealed associations with age 3years (OR: 0.27; 95%CI [0.09-0.85]; p-value 0.03), age 4years (OR: 0.21; 95%CI [0.06-0.73]; p-value 0.01),positiveparacheck test (OR: 6.11; 95%CI [2.76-13.51]; p-value < 0.001), using antimalarial drugs (OR: 3.53; 95%CI [1.89-6.62]; p-value <0.001) and underweight in children (OR: 3.04; 95%CI [1.25-7.42]; p-value 0.01). For haemoglobin concentration a multivariate model revealed association with sex and use of malaria drugs, showing that haemoglobin in female children was significantly higher than in male children by a mean of 0.35g/dl (Coeff: 0.35g/dl; 95%CI [0.02-0.68]; p-value 0.04) and for children on malaria drugs had significantly low haemoglobin concentration compared to those not on the drugs by a mean of 0.57g/dl (Coeff: -0.57g/dl; 95%CI [-0.91-0.22]; p-value 0.001) Conclusion: Anaemia is common in Handeni District. Further control of anaemia should focus on the control of malaria which is the major cause for anaemia. However, strategies for minimizing childhood anaemia should include improving nutritional status among children