The ongoing transfer of harmful organisms by shipping, especially via ballast water transport, may result in a change of biodiversity, alteration of ecosystems, negative impacts on human health and economic loss. Species introductions which cause irreversible consequences to receiving environments and economies call for particular attention. One critical issue is a need to evaluate the quantities and processes of species introductions. Consequently ballast water was sampled on 15 ships calling at the Port of Koper, Slovenia. This was the first ballast water sampling study in the Mediterranean Sea. This paper summarises the sampling results. Samples were analysed for all types of aquatic organisms including bacteria. The results may be considered as background information for an initial risk assessment of future species introductions - an important tool for the implementation of ballast water management measures.