Use of data generated through the Health Management Information System (HMIS) in decision making has been facing various challenges ever since its inception in Pakistan. This descriptive qualitative study attempts to explore the perceptions of health managers to identify the status and issues in use of HMIS. Overall 26 managers (all men, ages ranging from 26 to 49 years; selected from federal level (2), provincial (4) and seven selected districts (20) from all four provinces) were interviewed face to face. The respondents identified a number of hurdles resulting in non-use, misuse and disuse of data. These included limited scope of HMIS, dubious data quality, political motives behind demand of data and an element of corruption in data reporting etc. A great deal of political and administrative will is required to institutionalize transparency in decision making in health management and HMIS is an important tool for doing so. Appropriate legislation and regulations are needed to create a conducive policy environment that would help in changing the existing decision making culture. The effective use of information requires that besides capacity development of district health managers in understanding and use of data, the higher level decision makers are provided with relevant data timely and in an easily understandable form along with the recommended actions pertinent to this data.