The Port Authority of New York and New Jersey (PANYNJ) has adopted a policy to reduce its greenhouse gas (GHG) emissions by 80% by the year 2050. For this project, E. H. Pechan & Associates, Inc., and Southern Research Institute developed 2006, 2007, and 2008 calendar year GHG and criteria pollutant emission inventories for PANYNJ facilities and operations, including the emissions of its tenants (e.g., airlines and shippers) and patrons [e.g., airport passengers and Port Authority TransHudson (PATH) riders]. In addition, the consulting team developed and implemented systems that allow for annual tracking and reporting of GHG emissions. PANYNJ manages and maintains the bridges, tunnels, bus terminals, airports, PATH commuter rail system, and marine terminals that are critical to the metropolitan New York and New Jersey region's trade and transportation capabilities. Major facilities owned, managed, operated, or maintained by PANYNJ include John F. Kennedy International, Newark Liberty International, and LaGuardia Airports; the George Washington Bridge; the Lincoln and Holland Tunnels; Port Newark and the Howland Hook Marine Terminal; the Port Authority Bus Terminal; and the 16-acre World Trade Center site in lower Manhattan. This paper describes the methods used to develop consistent GHG and criterion pollutant emission estimates for a diverse set of source types and how these methods have been updated as new information and new protocols have emerged.