Tissue section replicates from lymphoid tissues and livers of gnotobiotic swine were examined by immunohistochemistry for the colocalization of porcine circovirus-2 (PCV-2) nucleocapsid and terminal deoxynucleotidyl transferase (TdT)-mediated incorporation of biotinylated nucleotides (UTP) onto the 3'-exposed hydroxyl groups (nick end labeling) nuclear deoxyribonucleic acid (TUNEL), a marker for apoptosis. Single- and dually stained replicates from uninfected controls, subclinically affected PCV-2-infected gnotobiotic pigs, PCV-2-infected piglets immunosuppressed with cyclosporine (Cys), and PCV-2-infected piglets with post-weaning multisystemic wasting syndrome (PMWS) were evaluated. Thymuses were used as positive controls for apoptosis absent PCV-2, tissue sections from dogs given hyperthermic stress were examined as positive controls for induced TUNEL. Tissues from heat-stressed dogs contained TUNEL-positive cell nuclei in both lymphoid tissues and liver, TUNEL was greatest shortly after the delivery of the hyperthermic insult. In uninfected control and subclinically affected PCV-2-infected gnotobiotic pigs, rare hepatocytes and lymphoid cells were TUNEL positive, the frequency of these was similar to that seen in uninfected controls. In PMWS-affected and Cys-treated PCV-2 piglets, the only consistent strongly positive TUNEL signal was contained within the cytoplasm of virus-positive phagocytic mononuclear cells. In phagocytes, some PCV-2 inclusions were TUNEL positive. Collectively, these data indicate that apoptosis is not the primary mechanism of lymphoid depletion and hepatocyte loss in PMWS. Apoptosis associated with systemic viral diseases may be attributable to pyrexia rather than direct or indirect effects of viruses on target cells.