The genome sequence of the protistan parasite Entamoeba histolytica HM-1:IMSS has been completed recently. Among the findings has been a unique organisation for the tRNA genes in this organism. Forty-two of the tRNA isoacceptor types are encoded in tandem arrays that vary in unit length from 490 to 1775 basepairs and contain from 1 to 5 tRNA genes. In three cases a 5S RNA gene is also present in the unit. An estimated 10% of the genome is made up of these arrays. Interspersed between RNA-encoding sequences are short tandem repeats that are polymorphic between isolates and, in some cases, within isolates. The number and organisation of tRNA genes in E. histolytica is unprecedented. In addition to encoding the tRNAs of the organism we propose that the arrays may fulfil a structural role in the genome.