Nowadays, 1.2 billion people still lack of access to electricity. Autonomous systems based on renewable energy sources are an appropriate alternative extend electrification, in particular for Ecuadorian Amazon Region (RAE). The objective of this work is to propose a tool to design of autonomous electrification systems for rural isolated communities of RAE, using photovoltaic technology and micro-grid or individual systems, and taking into account technical, economic and social aspects. For this purpose, a mixed integer linear programming model is developed that solves the type and number of equipment to install and where to place each of them, as well as the distribution micro-grids. The tool has been validated in the design of the electrification system of the community of Conambo.