Naegleria fowleri, Acanthamoeba spp., Balamuthia mandrillaris and Sappinia spp. are free-living amoebae that can infect humans and cause serious disease; therefore, these organisms are commonly referred to as pathogenic free-living amoebae (pFLA). Diagnosis and treatment of pFLA infections have historically been very challenging. If a diagnosis is made, treatment regimens currently include a combination of antifungals, antimicrobials and anticancer agents that have, to date, proven to be of little help in resolving the disease. Discovery of new therapies is critical to reduce the >90% mortality rate for the brain infections that these microbes can cause. Molecular tools that allow for the study of gene function, generation of reporter cell lines and drug target validation would greatly improve drug discovery efforts. To date, transfection approaches for use with pFLA have been limited, hindering these types of molecular studies. Based on sequence comparisons, the pFLA harbour proteins that are involved in cargo delivery to the nucleus and DNA repair mechanisms, suggesting that fundamental pathways believed to be required for stable transfection are present. However, the amoebae lack homologs to genes connected to stable maintenance of transgenes and RNA interference in other systems. While these differences may limit our ability to alter gene expression, it is also possible that unrecognized components fulfill the roles of the missing homologs. Given the value of robust transfection approaches in drug discovery and gene function studies, resolving these mechanisms would be impactful, leading to improved understanding of amoebae biology and enhancement of drug discovery efforts.