OBJECTIVES: This study was investigating of costs and consequences of two manual and computerized systems for management of information during 2008-2009 for inspection of pharmaceutical industries in Iranian Drug Regulatory Affairs. METHODS: To compute costs of processes following items had been considered: Cost of filling and archiving, data collecting (person-hour), reporting (person-hour),  transport, software, hardware (main server computer, pocket computer), stationeries. To evaluate the efficacy following outputs and outcomes was considered: Time of information recovering, ability of ranking, preventing of data missing, capacity building and tracking and monitoring.   RESULTS: The cost of running the new system is 35,000 US Dollars. Cost of education in new method and conventional are 5000 and 1000 US Dollars respectively.  Cost of inspection in computerized management of information system (MIS) is decreased to 250 US Dollars from 600 US Dollars for each inspection process. Alongside capacity of system is increased by arming to fast processing method, time of information recovering diminished to 1 working day instead of 3 days, preventing of data missing from 80% to 95% in new one, tracking and monitoring took 7 working days to applied, but new MIS changed that to 1 working day. Ranking of pharmaceutical industries is now available for Iranian Drug Regulatory Affairs after establishment of new inspection system by computer-based MIS.  CONCLUSIONS: It seems that beside overhead cost of new computerized system that is more than conventional method; considering capacity building; due to decreasing the cost of inspection and increasing of outputs and outcomes indicators, the new system is more efficient.