Physical methods and chemical modifications were used to discriminate between the bilirubin-binding capacity and glutathione-S-transferase activity of ligandin which was purified from rat liver. Binding of bilirubin occurs at a primary high affinity site (KA = 5 X 10(7) M-1) and at a secondary, lesser affinity site (KA = 3 X 10(5) M-1). Circular dichroism and fluorescence-quenching methods were used to distinguish between these sites. Cross-linked as well as reduced and alkylated ligandin lost high affinity bilirubin-binding capacity, but retained glutathione-S-transferase activity, bilirubin binding at a secondary site, and immunological reactivity. Succinylation of ligandin abolished catalytic activity and bilirubin binding at high and low affinity sites, but not immunological reactivity. Catalytic activity was unaffected by concentrations of bilirubin which saturated the primary binding site. These results suggest that the high affinity site at which bilirubin is bound to ligandin is independent from the site at which catalytically reactive substrates bind. The latter substrates probably interact at the secondary bilirubin binding site where bilirubin competitively inhibits glutathione-S-transferase activity.