Our findings have important implications for control of NiV in commercial pig farms, prevention of widespread epidemics in livestock and our general understanding of zoonotic disease emergence. First, although restrictions on planting fruit trees near pigsties appear to have prevented introduction of the virus into pig populations in Malaysia since 1999, there is a possibility of reintroduction both there and in other countries where flying foxes are found. Regular surveillance of pigs sent to markets and abattoirs in areas where pig farming overlaps flying fox distributions, along with hospital-based surveillance of encephalitis cases, may permit identification of initial NiV introductions and allow for early intervention and prevention of subsequent spread. Second, widespread prophylactic vaccination of pig populations is likely to be cost-prohibitive because of the rapid turnover of commercial pig populations. In addition, if vaccine coverage were not kept at a sufficient level, the dynamics of the virus when introduced into the population would resemble those following reintroduction on the index farm, inducing long-term persistence and increasing the risk of phase II emergence (electronic supplementary material).