Medical practice is shifting towards the automation and standardization of the most repetitive procedures to speed up the time-to-diagnosis. Semantic segmentation repre-sents a critical stage in identifying a broad spectrum of regions of interest within medical images. Indeed, it identifies relevant objects by attributing to each image pixels a value representing pre-determined classes. Despite the relative ease of visually locating organs in the human body, automated multi-organ segmentation is hindered by the variety of shapes and dimensions of organs and computational resources. Within this context, we propose BIONET, a U-Net-based Fully Convolutional Net-work for efficiently semantically segmenting abdominal organs. BIONET deals with unbalanced data distribution related to the physiological conformation of the considered organs, reaching good accuracy for variable organs dimension with low variance, and a Weighted Global Dice Score score of 93.74 ± 1.1%, and an inference performance of 138 frames per second. Clinical Relevance - This work established a starting point for developing an automatic tool for semantic segmentation of variable-sized organs within the abdomen, reaching considerable accuracy on small and large organs with low variability, reaching a 93.74 ± 1.1 % of Weighted Global Dice Score.