This report presents the results of surveillance activities on transmissible spongiform encephalopathies (TSEs) in bovine animals, sheep, goats, cervids and other species, as well as genotyping data in sheep, carried out in 2016 in the European Union according to Regulation (EC) 999/2001, and in Iceland, Norway and Switzerland. In 2016, 1,352,585 bovine animals were tested in the European Union (5% less than in 2015). For the first time, the United Kingdom did not report any case of bovine spongiform encephalopathy (BSE), whereas France reported one classical and three atypical cases (H), and Spain one atypical case (H). The classical BSE case was born after the enforcement of the total EU‐wide feed ban in 2001 (BARB case). In 2016, 286,351 sheep and 110,832 goats were tested (5% and 11% less than in 2015, respectively). Sheep scrapie was reported by 20 Member States (MSs) (685 cases) and goat scrapie by 9 MSs (634 cases). A total of 25 ovine scrapie cases were reported by Iceland and Norway. At the EU level, the occurrence of scrapie in small ruminants remains stable, with classical scrapie (1,175 cases) being reported more frequently than atypical scrapie (135 cases). A total of 97.2% of the classical scrapie cases in sheep occurred in animals with genotypes belonging to the susceptible group, and a random sampling showed that 26.6% of the genotyped sheep held genotypes of the susceptible group (excluding Cyprus). In 2016, five cases of chronic wasting disease were reported in cervids by Norway: three in wild reindeer and two in moose. It was the first time that this disease is reported in Europe. A total of 2,712 cervids were tested for TSEs in seven different member states, 90% of them in Romania, with negative results. A total of 490 animals from other non‐ruminant species were tested in four different member states, with negative results.