In epidemiological studies, several diseases share common risk factors or co-exist in their spatial prevalence. Disease mapping allows the health practitioners and epidemiologists to hypothesize the disease aetiology and gain better understanding of the geographical prevalence of the disease risks. This paper investigates the differences in small scale geographical variations and the underlying risk factors of child's health outcomes (anemia, stunting and wasting) in Sub-Saharan Africa using spatial epidemiology. The study first carried out an independent univariate analysis on each malnutrition indicator to identify underlying risk factors. A multivariate conditional autoregressive prior was explored to jointly model the spatial correlation between the undernutrition indicators and the small area-geographical disparities at sub-national levels in two sub-Saharan African countries. The approach was implemented on data from National cross-sectional household- based demographic and health surveys conducted in 17,307 under-five children in Burkina Faso and Mozambique in 2010-012. Out of these children, 31.8% are found to be stunted, 15.5% wasted and 30.9% had anemia among Burkina Faso children, while 42.5% of Mozambican children were stunted, 5.9% wasted and 30.9% suffered from iron-deficiency anemia. The multivariate analysis revealed that the spatial prevalence existed across regions in Burkina Faso with geographical variations in stunting estimated as: 0.7549, CI (0.4693, 1.264); wasting 0.9197; (95%CI: 0.535, 1.591)and anemia: 0.734; (0.4606, 1.214). In additin, the spatial correlation between stunting and wasting was negatively correlated: -0.998; 95% CI (-1.000, -0.984), and a perfect negative correlation;(-1) between stunting and anemia, and positive for wasting and anemia: 0.997; (0.978, 1.000). The spatial occurrence across provinces in Mozambique indicated that there was strong positive correlation between stunting and wasting; 0.986; (0.899, 1.000) and a significant negative correlation between stunting and anemia: -0.720, (-0.934, -0.308) and wasting and anemia: -0.640; (-0.903 -0.174) with individual geographical variability in child stunting: 1427, (913.6, 2268); wasting:1751, (1117, 2803) and anemia: 556, (279.5, 978.9). These extra random effect parameters computed in our multivariate approach would outperform a univariate analysis in similar studies. Our model further detected high prevalent of malnutrition and anemia in the northern Burkina Faso, but high anemia prevalent found in central Mozambique, and high stunting and wasting identified Southern Mozambique. In addition, the risk factors of malnutrition and iron deficiency anemia included household poverty, morbidity, short birth interval (less 18 months), breast feeding, antenatal attendance and maternal literacy. The statistical relevance of the identified risk factors in this study is useful to target specific individual interventions and the maps of the geographical inequalities in sub-national region can be used for designing nutrition interventions and allocation of scarce health resources.