Plant diseases are major obstacles in achieving optimal yields in crop plants including rice. The use of diseases-resistant varieties is one of the most practical and economical approaches to overcome this problem. The local rice populations (landraces) are important genetic resources containing useful genes for many important traits, including disease resistance characters. The objectives of this study were to evaluate the responses of East and North Kalimantan local upland rice population against rice diseases and to select the local cultivars having resistance against the diseases. Disease resistance was evaluated using natural disease epidemic selection. A 109 Indonesian local upland rice cultivars were grown in two different growing conditions, in screen house and field trial. Diseases were characterized by their symptoms on the plants and the corresponding causing agents. Disease intensity was scored by observing the percentage of disease symptoms on the plants in the field trial. The results showed that bacterial blight (Xanthomonas oryzae) was the most frequent disease infecting East and North Kalimantan local upland rice population followed by narrow brown spot, brown spot, sheath blight and black kernel. A specific interaction between the host and pathogen was observed in this study. Some genotypes were resistant, and some others are susceptible to the particular disease. However, most of the local rice cultivars were grouped into resistant and moderately resistant genotypes. The East and North Kalimantan local upland rice population characterized in this study, contained genes that confer resistance to one or more pathogens, which could be further used as a source of vertical or horizontal resistance genes in rice breeding programs.