Current research and policies on reproductive behaviours in many East African countries focus primarily on proxy indicators of women’s autonomy, and very little emphasis is placed on direct indicators of women’s autonomy. In this paper, data from the 2002 Eritrea Demographic and Health Survey (EDHS) are used to address some of the most frequently raised questions about the link between women’s autonomy and reproductive behaviour. The results from the multivariate logistic models show that although the relationship between women’s autonomy and reproductive preferences in Eritrea is complex, some clear, broad patterns exist that have implications for theory and policy. First, although the different dimensions of women’s autonomy influence the outcome variables differently in terms of magnitude and statistical significance, most of them have a strong connection; in particular, women’s final say in decisions regarding day-to-day household purchases and spousal communication are significant explanatory variables in fertility preferences and ever-use of modern contraception. Second, many background (proxy) variables, particularly household economic condition and employment, exert a strong and independent influence over fertility preferences and ever-use of contraception regardless of a woman’s autonomy. In their relationship to reproductive behaviours, therefore, employment and economic status cannot be considered as proxies for women’s autonomy in Eritrea. A complete explanation of the relationship between women’s autonomy and reproductive preferences must recognize the effects of both the background and direct autonomy indicators. Interventions are needed to improve women’s decision-making autonomy and strengthen their negotiating capacity on family planning if an increased desire to limit fertility is to be attained.