The influence of structural modifications on NM toxicity, and in particular structural defects, is poorly studied mainly because of the difficulty to modify the crystallinity of a NM without changing any other morphological parameters. In this study we used a singled-walled alumino-germanate nanotube (Ge-imogolite) as a model, for which this can be achieved. Well crystalized tubes led to moderate toxicity attributed to a direct contact with the bacteria and the generation of reactive oxygen species, whereas lacunar tubes caused more severe toxic effects without any direct contact nor ROS generation. The bacterial growth inhibition in the presence of wall defects was attributed to indirect mechanisms as their higher solubility leading to Al or Ge ion toxicity and/or to the retention of essential nutrients on the vacancies