The fragile X syndrome is the most frequent cause of inherited mental retardation. Advances in understanding the molecular basis for this syndrome have elicited new prospects for identifying a greater number of individuals at risk for the disorder. Features of direct DNA analysis along with the high frequency of fragile X gene carriers have generated interest for population-based screening. Methods: We have evaluated four potential screening periods for the fragile X syndrome and discuss advantages and limitations in each. These periods include: newborn, prenatal, women considering pregnancy and developmentally delayed school-aged children. Economic evaluations, diagnostic tests and the interests and needs of the specific population are considered to assess the feasibility of screening programs. Results and discussion: The complex nature of the fragile X mutation and inheritance pattern present difficult dilemmas when considering population-based screening. Each population has both advantages and limitations of screening with respect to the issues we discussed. Clearly, further basic research is needed to answer questions concerning the mechanism of gene expansion and expression. However, the potential for fragile X screening can be considered only if pilot studies have been conducted to study the resources required to ensure appropriate testing and follow-up services in addition to uncovering unanticipated medical, legal and ethical problems.