Aquaculture is an important segment of Croatian fishing industry with long tradition of carp and rainbow trout farming as well as marine aquaculture represented by shellfish (flat oyster and mussels), sea bass and sea bream cultivation and Atlantic bluefin tuna fattening. The fish and shellfish diseases survey is regulated by “Decree on the measures of animal health protection against infectious and parasite diseases” issued yearly by Ministry of Agriculture. This report derives from systematic clinical, parasitological, pathoanatomical, histopathological, bacteriological and virological monitoring of cultivated fish and shellfish on larger part of production during last several years. Among pathological conditions recognised on our farms, some specific viruses, bacteria and parasites represent frequently established causative nosologic agents. The overview of the main diseases with economic impact to the cultivation will be discussed in this paper.