At the request of Malta’s Infectious Disease Prevention and Control Unit (IDCU), the European Centre for Disease Prevention and Control (ECDC) organized an expert mission in Malta in 2009 to provide support for a vector-borne disease (VBD) risk assessment. As these diseases are clearly related to the presence of competent and efficient vectors, and as little information was available on the local mosquito fauna (Diptera: Culicidae), a field study was implemented during the mission. The aim was to determine the presence and relative abundance of potential vectors, and to assess the risk of transmission of mosquito-borne diseases. From April 6th to May 1st, 2009, a total of 114 among 513 investigated putative larval habitat units contained mosquito immature stages. Artificial habitats and coastal saltwater rock pools predominated among the larval habitats. Also, 1,150 female mosquitoes were caught with dry-ice baited light traps. Seven species among the nine known to occur in Malta at the time of the study were observed and Culex theileri is reported here for the first time. The most commonly encountered species were Culiseta longiareolata and Culex pipiens. Culex hortensis was only found on the island of Gozo. The mosquitoes of the Mariae complex have been identified in the past as Aedes zammitii but all except four of the specimens collected showed morphological characters corresponding to Aedes mariae. Neither Anopheles spp. nor Aedes albopictus were found despite the investigation of suitable larval habitats and the use of CO2-baited light traps and a few ovitraps. However, these species are known to be more abundant during the summer months and further investigations are needed to confirm their absence or their presence and distribution on the islands. The mosquito-related risk of disease for humans in Malta is discussed and West Nile fever appears to be the most probable mosquito-borne disease that could appear in Malta. The eventual finding of Aedes albopictus after this study was completed further strengthens the need to survey both chikungunya and dengue infections.