A survey of rice growing regions in East Timor (Timor Leste) conducted in 2010 has resulted in the identification of several bacterial species associated with sheath browning and seed discolouration. Bacteria were identified by partial sequencing of the 16s rRNA gene and comparison with sequences from GenBank and EZtaxon databases. Bacterial isolates of known pathogens of rice, corn and cotton were identified, along with non-phytopathogenic endophytes. This is an indication that the disease symptoms are likely to be the result of a pathogen complex rather than caused by a single species. Unfortunately, due to current lack of infrastructure in East Timor, definitive pathogenicity testing of these isolates could not be undertaken. However, it is imperative to increase the capacity of East Timorese to improve their diagnostic skills and management of diseases of rice, and ultimately increase productivity. Furthermore, it is important to heighten the awareness of East Timorese farmers of the importance of diseases in rice production. Evidently, there is a potential source of high risk bacterial pathogens in the rice production system in East Timor and this also poses a risk to Australia's biosecurity. Potentially devastating pests and diseases of Australian agriculture currently present in Asia could spread into Australia via East Timor. There are a number of economically important diseases of rice that occur in Southeast Asia which do not currently occur in Australia.