The importance of ciliates as a trophic link, which is defined as a fraction of the energy bound by primary producers that is transferred through the ciliate community, was assessed in the pelagic zones of shallow, eutrophic, and estuarine lakes. The study was conducted in Lake Gardno and Lake Łebsko located in northern Poland. Each of these lakes is characterized by very high mean annual ciliate biomasses of 115 μg C-1 (Lake Gardno, April 2006 – April 2007), 107 μg C L-1 (Lake Gardno, February 2007 – February 2008), 85 [mu]g C L-1 (Lake Łebsko, April – November 2007), and 127 μg C L-1 (Lake Łebsko, April – September 2008). Ciliate production was estimated using allometric equations and was compared to primary production measured with the light-and-dark bottles method. Annual, depth-integrated ciliate secondary production corresponded to 9 and 11% (Lake Gardno, two consecutive years studied) and 12% (Lake Łebsko, the same value for two growing seasons studied) of primary production. These values exceed the majority of other estimates in the literature, which indicates the high importance of ciliates in such highly-productive, shallow lakes.