Abundance, biomass, and taxonomic composition of the ciliate community were studied in the surface waters along a transect between 50°S 61°W and 48°N 5°W (Atlantic Ocean, March-April 2011). The abundance of heterotrophic ciliates was low in the equatorial zone (280–320 cells l−1, 0.11–0.12 μg C l−1), but it increased toward both the northern and southern temperate zones with the maximum abundance observed at 44°S (2667 cells l−1, 0.82 μg C l−1). This pattern resembles the global distribution of oceanic primary production, which is low at lower latitudes and high in temperate zones. In temperate zones ciliate abundance peaks during spring and fall. Thus, because the present study was carried out during spring in the northern hemisphere and austral fall in the southern hemisphere, the ciliate abundance at higher latitudes was additionally elevated. Functionally autotrophic Mesodinium rubrum was only observed in the northern hemisphere and tropical waters. Its maximum abundance was observed at 48°N (1080 cells l−1, 1.14 μg C l−1). The most frequently observed ciliates were oligotrichs and choreotrichs. Other important ciliates were haptorids (including M. rubrum) and hypotrichs.