Invasive alien species (IAS) have been recognized as one of the major threats to native biodiversity in the Danube Basin. The aim of this paper is to present the state of the art regarding IAS along the Danube River and its main tributaries. The work is mainly based on the results of the Danube research expeditions, Joint Danube Survey 2 (2007), Joint Danube Survey 1 (2001) and AquaTerra Danube Survey (2004), but other recent data on IAS were taken into consideration, as well. The complexity of the problem with IAS could be illustrated by the fact that six species of neophytes, 19 alien macroinvertebrates and 15 non-native fish species were recorded during JDS2. The total number of alien species recorded, as well as their frequency and abundance along the Danube, indicates high level of biological contamination. Despite the fact that IAS have been in the focus of the research in the Danube Basin for the last 15 years, we still do not have enough data on their exact distribution and migration. A lot of additional work concerning detection, monitoring, assessment of their impacts and management is necessary in order to deal with the IAS problem properly in river basin management planning.