BACKGROUND Fibroblasts are critical to the establishment and maintenance of the periodontal attachment apparatus (cementum, periodontal ligament [PDL], and bone). In order to characterize the cellular changes that accompany periodontal regeneration, better tools are necessary to distinguish periodontal ligament fibroblasts (PDLF), gingival fibroblasts, and osteoblasts. Our goal is to identify gene markers to better characterize and identify these cell types. METHODS We chose to examine and compare the expression of numerous gene transcripts by semiquantitative reverse transcriptase-polymerase chain reaction using primers specific for 44 different gene transcripts in order to better characterize the identity of these cells. RESULTS Several transcripts were cell-type specific. Specifically, fibromodulin was expressed only in PDL fibroblasts, while osteopontin was expressed only in dermal fibroblasts. In addition, lumican was expressed by all three types of fibroblasts (PDL, gingival, and dermal), while alkaline phosphatase was expressed by osteoblasts as well as PDL and gingival fibroblasts. CONCLUSIONS Our results indicate that PDL fibroblasts are distinct from either gingival or dermal fibroblasts or osteoblasts. In general, PDL and gingival fibroblasts displayed greater similarity to each other than either displayed toward dermal fibroblasts. Furthermore, both gingival and PDL fibroblasts displayed greater similarity to osteoblasts than to dermal fibroblasts, possibly reflecting their common origin (the neural crest).