This research uses the latest Demographic and Health Surveys to investigate the heterogeneity of effects of socioeconomic and cultural factors on fertility preferences in Rwanda and Kenya, two countries undergoing fertility transition. The results show that the preference for high fertility in Rwanda is associated with few factors namely low education, protestant religion and high child mortality. In this country, economic factors are not significant. In Kenya, however, both socioeconomic and cultural factors are important. The propensity for high fertility is correlated with low economic status, low education, Muslim religion, large family size of origin, high child mortality, etc. While Rwanda tends to be homogenous with the attitude towards low fertility Kenya displays enormous variations. The negative attitude for high fertility in Rwanda, even among the poor and rural populations, has been linked with poverty awareness and scarcity of land, which undermine the traditional values attached to large families. The conclusion is that the relationships between socioeconomic and cultural factors and fertility preferences are not unidirectional; they may vary with local context. What is significant in one country may be with less important in another. Thus, the strategies to enhance the ongoing fertility transition should be country based, designed and implemented.