The emu (Dromaius novaehollandiae) occupies most regions of the Australian continent and in recent times has been farmed for meat, oil, and leather. Very little is known about the genetic structure of natural or farmed populations of these birds. We report a preliminary study of genetic variation in emus undertaken by typing birds from five farms and two natural populations at five polymorphic microsatellite loci. Genetic diversity was high for all populations and there was little evidence of inbreeding, with most populations conforming to Hardy-Weinberg equilibrium for most loci. Significant heterozygote deficiencies at one locus in a number of populations were detected and may indicate the presence of null alleles. Comparisons of allele frequencies showed little evidence of genetic differentiation either among farmed populations or between farmed and natural populations.