Four measurement campaigns were performed in two different environments – inside the harbour areas in the city centre of Helsinki, and along the narrow shipping channel near the city of Turku, Finland – using a mobile laboratory van during winter and summer conditions in 2010–2011. The characteristics of gaseous (CO, CO<sub>2</sub>, SO<sub>2</sub>, NO, NO<sub>2</sub>, NO<sub>x</sub>) and particulate (number and volume size distributions as well as PM<sub>2.5</sub>) emissions for 11 ships regularly operating on the Baltic Sea were studied to determine the emission parameters. The highest particle concentrations were 1.5 × 10<sup>6</sup> and 1.6 × 10<sup>5</sup> cm<sup>−3</sup> in Helsinki and Turku, respectively, and the particle number size distributions had two modes. The dominating mode peaked at 20–30 nm, and the accumulation mode at 80–100 nm. The majority of the particle mass was volatile, since after heating the sample to 265 °C, the particle volume of the studied ship decreased by around 70%. The emission factors for NO<sub>x</sub> varied in the range of 25–100 g (kg fuel)<sup>−1</sup>, for SO<sub>2</sub> in the range of 2.5–17.0 g (kg fuel)<sup>−1</sup>, for particle number in the range of (0.32–2.26) × 10<sup>16</sup> # (kg fuel)<sup>−1</sup>, and for PM<sub>2.5</sub> between 1.0–4.9 g (kg fuel)<sup>−1</sup>. The ships equipped with SCR (selective catalytic reduction) had the lowest NO<sub>x</sub> emissions, whereas the ships with DWI (direct water injection) and HAMs (humid air motors) had the lowest SO<sub>2</sub> emissions but the highest particulate emissions. For all ships, the averaged fuel sulphur contents (FSCs) were less than 1% (by mass) but none of them was below 0.1% which will be the new EU directive starting 1 January 2015 in the SO<sub>x</sub> emission control areas; this indicates that ships operating on the Baltic Sea will face large challenges.