The amitochondriates are an assembly of unicellular protists that lack mitochondria, and often other typical eukaryotic organelles, such as peroxisomes. Relatively little research has been conducted on amitochondriates, even though marine waters are likely to be teeming with such organisms, representing yet unknown protist lineages. The three amitochondriates that have been studied in any detail are the three mucosal human parasites: Giardia, Trichomonas and Entamoeba. These pathogens have worldwide distribution and are the most commonly encountered parasites in North America and Europe. Despite significant differences in their lifecycles and pathogenic properties, Giardia, Trichomonas and Entamoeba are customarily grouped together based on their being microaerophilic, their anaerobic carbohydrate metabolism, their lack of mitochondria, and their placement on deep-branching lineages in eukaryotic phylogenetic trees. During the last decade, the development of functional tools has allowed molecular analyses of gene expression to be initiated on these divergent eukaryotes. The resulting data indicate significant differences between the organisation of genetic information and mechanisms of gene regulation in amitochondriates and other organisms. Promoter architecture, as well as the regulatory transcription factors required to mediate promoter activity, lacks the conservation observed for the transcriptional apparatuses of metazoa and even appear to be unique within the amitochondriates. Our knowledge of the molecular biology and gene expression in amitochondriates is still in its infancy and a discussion of the current status of research in this area is presented.