This research aims to provide empirical evidence regarding the effect of capital structure, family ownership, and the effectiveness of board of commissioners and audit committee on the efficiency in manufacturing company. Efficiency is measured by Data Envelopment Analysis (DEA) score, while the effectiveness of board of commissioners and audit committee are measured by effectiveness measurement method which was developed by Hermawan (2009). The hypothesis are examined using panel data regression with fixed effect method to a sample of 100 manufacturing companies listed in Indonesian Stock Exchange during 2008 to 2012. The result of this research concludes that companies with higher leverage could gain higher efficiency in their operation. The companies with higher effectiveness of board of commissioners also could gain higher efficiency in their operation. Meanwhile, family ownership and the effectiveness of audit committee have no significant impact to efficiency in the companies.