Zeolites are aluminosilicate materials that contain regular three-dimensional arrays of molecular-scale pores, and they can act as hosts for catalytically active metal clusters(1). The catalytic properties of such zeolites depend on the sizes and shapes of the clusters, and also on the location of the clusters within the pores. Transmission electron microscopy has been used to image single atoms and nanoclusters on surfaces(2), but the damage caused by the electron beam has made it difficult to image zeolites(3,4). Here, we show that aberration-corrected scanning transmission electron microscopy can be used to determine the locations of individual metal atoms and nanoclusters within the pores of a zeolite. We imaged the active sites of iridium catalysts anchored in dealuminated HY zeolite crystals, determined their locations and approximate distance from the crystal surface, and deduced a possible cluster formation mechanism.