A simple 2-step method to selectively quantify functional bradyzoites of Toxoplasma gondii is described. The method was developed to quantify bradyzoites produced in cell cultures that also contain tachyzoites. The selection step comprises incubation of bradyzoites and tachyzoites in 0.026% pepsin at 37 C for 30 min. This treatment kills all tachyzoites, whereas all bradyzoites survive. A modified plaque assay is then used to quantify the surviving bradyzoites. Plaque assay cultures are scored according to levels of infection that correlate with numbers of bradyzoites added to each well. The assay can detect log differences in the range of 2 x 10(0)-2 x 10(4) bradyzoites per sample. This procedure is simple to perform and provides an efficient way of comparing numbers of functional bradyzoites in multiple samples that also contain tachyzoites.