The growing incidences of drug-resistant pathogens have increased the attention on several medicinal plants and their metabolites for antimicrobial properties. These pathogens are the main cause of nosocomial infections which led to an increasing mortality among hospitalized patients. Taking into consideration those factors, this paper reviews the state-of-the-art of the research on antibacterial agents from native Brazilian plant species related to nosocomial infections as well as the current methods used in the investigations of the antimicrobial activity and points out the differences in techniques employed by the authors. The antimicrobial assays most frequently used were broth microdilution, agar diffusion, agar dilution and bioautography. The broth microdilution method should be the method of choice for testing new antimicrobial agents from plant extracts or isolated compounds due to its advantages. At the moment, only a small part of the rich Brazilian flora has been investigated for antimicrobial activity, mostly with unfractionated extracts presenting a weak or moderate antibacterial activity. The combination of crude extract with conventional antibiotics represents a largely unexploited new form of chemotherapy with novel and multiple mechanisms of action that can overcome microbial resistance that needs to be further investigated. The antibacterial activity of essential oil vapours might also be an interesting alternative treatment of hospital environment due to their ability in preventing biofilm formation. However, in both alternatives more studies should be done on their mode of action and toxicological effects in order to optimize their use.