Background: Organizational silence has irreparable consequences for the organization, since withholding ideas (silence) will stop employees' minds from generating organizational knowledge. Therefore, this study aimed at identifying the factors affecting organizational silence among middle managers as well as providing solutions to this problem. Methods: The present qualitative research was conducted through content and thematic analysis. The viewpoints of the managers of Shiraz University of Medical Sciences during years 2016 and 2017, were collected using the purposeful sampling method. The findings were saturated after conducting ten semi-structured interviews. Results: The findings of the research showed that factors affecting organizational silence among middle managers of the university were categorized to: (1) organizational factors (including three main themes: (a) organizational structure and process, (b) organizational communication, (c) organizational culture); and (2) and individual factors (including three main themes: (a) psychological factors, (b) communication skills, and (c) demographic factors). Conclusions: The findings showed that organizational silence exists among university mangers and reduces the effectiveness of decision-making and organizational change processes due to restricting the amount of data provided for decision makers.