BACKGROUND: Heparan sulfate (HS) is an important component of many extracellular matrices that interacts with mitogens and morphogens to guide and control tissue and organ development. These interactions are controlled by its structure, which varies when produced by different cell types and different species. The major aim of the studies reported here was to isolate and characterize the HS expressed on the N-terminal domain of human perlecan when it is expressed in human cells. RESULTS: The recombinant proteoglycan was expressed in greatest quantities when the cells were grown as monolayers in the presence of Medium 199. It was purified as a proteoglycan with a molecular weight between 75 and 150kDa, which was decorated with HS, chondroitin sulfate (CS) and keratan sulfate (KS) in a similar way to the full-length perlecan from the same cells. Compositional analysis of the glycosaminoglycan (GAG) chains suggested that it contained the same amount of CS and HS, suggesting that one of the attachment sites may not be glycosylated. The HS chains were responsible for the binding of fibroblast growth factor 2 (FGF2), while the specific roles of the CS and KS remain unclear. CONCLUSION: Expressing the N-terminal domain of the proteoglycan perlecan results in a hybrid truncated molecule that binds to growth factors via it's HS and may prove useful to add to scaffolds to encourage cells to respond to growth signals, such as those produced by the FGFs. (c) 2008 Society of Chemical Industry.