The neurotropic bird schistosome Trichobilharzia regenti possesses papain-like cysteine peptidases which have also been shown to be crucial enzymes in various developmental stages of the related human parasites Schistosoma spp. In this paper, we present data obtained by real-time polymerase chain reaction on the temporal distribution of transcripts of two cathepsins in different developmental stages of T. regenti: cathepsin B1 originally described from the gut lumen of schistosomula with presumptive role in nutrient digestion and cathepsin B2 originally found in penetration glands of cercariae with probable involvement in invasion of the final host. In spite of their mutual resemblance at the sequence level, the mRNA expression profiles clearly show distinct expression of cathepsins B1 and B2 during the development from eggs to cercariae. In the case of both cathepsins, the highest level of transcription was detected in intravertebrate stages. Putative functions of cathepsins B1 and B2 in schistosome developmental stages are discussed.