The prevention and control of new pest and disease introductions is an agricultural challenge which is attracting growing public interest. This interest is in part driven by an impression that the threat is increasing, but there has been little analysis of the changing rates of biosecurity threat, and existing evidence is equivocal. Traditional biosecurity systems for animals and plants differ substantially but are beginning to converge. Bio-economic modelling of risk will be a valuable tool in guiding the allocation of limited resources for biosecurity. The future of prevention and management systems will be strongly influenced by new technology and the growing role of the private sector. Overall, today's biosecurity systems are challenged by changing national priorities regarding trade, by new concerns about environmental effects of biological invasions and by the question ‘who pays?’. Tomorrow's systems may need to be quite different to be effective. We suggest three changes: an integration of plant and animal biosecurity around a common, proactive, risk-based approach; a greater focus on international cooperation to deal with threats at source; and a commitment to refocus biosecurity on building resilience to invasion into agroecosystems rather than building walls around them.