An alignment between two or more aspect in hospitals could have an impact on efficiency. The results of a preliminary study at 9 regional general hospitals showed an inefficient 66.67% in 2015-2016, and there was a decrease in efficiency 33.33% of the inefficient hospital. The purpose of this paper is to analyze the contribution of alignment between the costs of quality improvement activities and quality achievements on efficiency in hospital. This study is an observational analytic research with survey method. The population of this study is general hospitals (government and private) class B and C in East Java of 150 units with a sample of 30 hospitals. Respondents for the alignment assessment are 432 people, while for the efficiency measurement are 118 people. Analysis to determine the contribution of alignment on efficiency using linear regression statistical test. The results showed that most hospitals were in an align between the cost of quality improvement activities with quality achievement of 70%, most of the hospitals were in the efficient of 60%, and the contribution of alignment between the costs of quality improvement activities and quality achievement on efficiency (RoS /CoS ratio) of 4.1% with a value of R² = 0.041. The conclusion was the contribution of alignment between the costs of quality improvement activities and quality achievements on efficiency was only small, and in fact the contribution (effect) of other than alignment was very large. Recommendation, hospital management cannot be partial but must be comprehensive.