The performance of HVAC systems may fail to satisfy design expectations due to equipment degradations, incorrect control sequences or sensor failures. Retro-commissioning identifies and implements cost-effective operational and maintenance improvements in existing buildings to bring the buildings up to the design intents. In this study, Building 90 at LBNL is used as a case study to demonstrate the processes of retro-commissioning. Building energy benchmarking tools are applied to evaluate the energy performance for screening process at the whole building level. The building benchmarking results indicated a large energy saving potential for gas consumption. Through the reviewing process of architectural drawings, mechanical drawings, equipment specifications, EMCS control sequences and trend data analyses for two representative seasons, summer and winter, several problems including faulty operations of air side economizers, simultaneous heating and cooling, substantial imbalance between supply air flow rate and return air flow rate are identified. A series of functional testing was conducted to verify the outdoor air damper leakage, building static pressure during system operations, and air flow imbalance. Energy saving potential is estimated for retro-commissioning measures. In the presentation, lessons learned from retro-commissioning procedure and the possibility of integrating automatic fault detection and diagnostic with EMCS will also be discussed.