This study addresses the exhaust emissions of CO₂, NO(x), SO(x), CO, and PM(2.5) originated from Baltic Sea shipping in 2006-2009. Numerical results have been computed using the Ship Traffic Emissions Assessment Model. This model is based on the messages of the automatic identification system (AIS), which enable the positioning of ships with a high spatial resolution. The NO(x) emissions in 2009 were approximately 7 % higher than in 2006, despite the economic recession. However, the SO(x) emissions in 2009 were approximately 14 % lower, when compared to those in 2006, mainly caused by the fuel requirements of the SO(x) emission control area (SECA) which became effective in May 2006, but affected also by changes in ship activity. Results are presented on the differential geographic distribution of shipping emissions before (Jan-April 2006) and after (Jan-April 2009) the SECA regulations. The predicted NO(x) emissions in 2009 substantially exceeded the emissions in 2006 along major ship routes and at numerous harbors, mostly due to the continuous increase in the number of small vessels that use AIS transmitters. Although the SO(x) emissions have been reduced in 2009 in most major ship routes, these have increased in the vicinity of some harbors and on some densely trafficked routes. A seasonal variation of emissions is also presented, as well as the distribution of emissions in terms of vessel flag state, type, and weight.