The technique of reverse transcription-PCR for mRNA phenotyping was applied to total RNA isolated from the two compartments of cancellous bone, namely trabecular bone and hematopoitic tissue or marrow. The pattern of gene expression for ten different growth factor ligands and five growth factor receptors was examined in total RNA isolated from the two compartments of cancellous bone of the female rat distal femur. Our results show that transcripts encoding IGF-I, IGF-II, transforming growth factor-β1 (TGF-β1), TGF-α, basic fibroblast growth factor, platelet-derived growth factor A and osteocalcin are detectable in samples from both trabeculae and marrow. Expression of epidermal growth factor (EGF) was confined to samples from trabeculae while nerve growth factor expression was only detected in marrow. Transcripts encoding insulin were not detected in any of the bone-derived samples in this study. Samples from cancellous bone trabeculae and marrow both showed evidence of expression of the genes encoding receptors for IGF-I, parathyroid hormone (PTH)/PTH-related protein and insulin. Neither compartment of cancellous bone contained transcripts encoding the receptor for IGF-II. Transcripts encoding the EGF receptor were detected in samples from cancellous bone marrow and not trabeculae as has been previously reported. These patterns of growth factor ligand and receptor gene expression suggest that it is likely that both autocrine and paracrine regulatory circuits are established in cancellous bone. This study also demonstrated the feasibility of assessing the expression of multiple genes from the small samples of total RNA obtained from separated tissues of cancellous bone. This is the first time that growth factor gene expression has been examined in separated trabeculae and marrow from cancellous bone and this approach will allow a more detailed analysis of molecular events in cancellous bone as opposed to whole bone or extracts of isolated and cultured bone cells.