Macro- and micro-structures of granules, developed in an upflow anaerobic acid reactor, were examined by light and electron microscopy. Every granule was found to be white, soft and non-spherical and had an open cavity at the centre. Scanning electron microscopy showed that the granules were composed of rod-shaped bacteria, of different thicknesses and lengths, arranged in three distinct layers within the granules. Transmission electron microscopic analysis of ultra-thin sections of granules, stained with Ruthenium Red, revealed the presence of extra-cellular polymeric materials around the cells. Gram staining tests confirmed the presence of both Gram-positive and Gram-negative bacteria in the granules. The intertwined nature of the bacterial arrangement in the granules and the extracellular polymeric substance that encapsulated the cell colonies contributed to the structural stability of the granules. © 2011 Taylor & Francis.