This study was undertaken to assess the prevalence of anaemia and to investigate various factors associated with haemoglobin (Hb) prevalence in children aged 6–59 months in Ghana. The data set used was based on a longitudinal study from the fourth round Multiple Indicator Cluster Survey (MICS). This was a national survey conducted by Ghana Statistical Service (GSS) to monitor the progress of women and children. A sample of 7,626 children under-five years across the country between 2009 and 2011 were selected for the survey. Multiple logistic regression and bootstrap technique for parameter estimates were used to determine the relationship of biological, socio-economic, nutritional and other factors associated with Hb concentration. The prevalence of anaemia among children between 6 – 59 months in Ghana found in this study was 64.7% which is quite high even though lower than the 2008 GDHS rate of 78%. This is so because it is still higher than the WHO cut-off point of 40% making it a serious public health concern. The highest rate of 36.2% occurs within the 6 – 23 months. The factors observed to be highly significantly associated with anaemia among these children included malaria prevalence (p-value=0.000), age of the child (p-value=0.000), household economic status (0.000), region of residence (p-value=0.000), mothers educational level (p-value=0.000) and sex of the child (p-value=0.000). All other factors considered such as area of residence and ethnicity were not significant (p-values > 0.05). In a nutshell, children who are born to more advantaged women who have high educational levels, economically sound, live in areas that are not infested with malaria, live in the southern part of Ghana and are females have low probability of becoming anaemic than their counterparts who are disadvantaged and live in malaria prone environment.