Immunoelectron microscopy is used in cell biological research to study the spatial distribution of intracellular macromolecules at the ultrastructural level. Colloidal gold particles (immunogold markers) are commonly used to localise molecules of interest on ultrathin sections and can be visualised in transmission electron micrographs as dark spots. Quantitative analysis involves detection of the immunogold markers, and is often performed manually or interactively as part of a stereological estimation technique. The method presented in this paper automatically detects and counts immunogold markers, estimating the location, size and type of each marker. It was evaluated on single-labelled as well as double-labelled images showing markers of two different sizes. This is a first step towards automatic analysis of immunoelectron micrographs, enabling a rapid and more complete quantitative analysis than is currently practicable. (C) 2011 Elsevier Inc. All rights reserved.