Background The semaphorin family is a large group of proteins initially described in axon guidance. However, semaphorins also play a role in other processes such as the regulation of immunity, angiogenesis, apoptosis and cell migration and invasion. Moreover, semaphorins have been related with the pathogenesis of multiple sclerosis, myocarditis, atherosclerosis and cancer. However, the potential role of class 3 semaphorins in rheumatoid arthritis (RA) remains unknown. The aim of this study is analyse the role of class 3 semaphorins in the pathology of RA. Methods mRNA expression of class 3 semaphorins in the synovial tissue of early, DMARD-naive arthritis patients and RA FLS was analysed by qPCR. FLS were stimulated with semaphorin (Sema)3A, Sema3B or Sema3F in the presence or absence of platelet-derived growth factor (PDGF) and cell migration and invasion were determined using wound closure motility and transwell invasion assays. Results mRNA expression of class 3 semaphorins in the synovial tissue of early arthritis patients negatively and significantly correlated with the mRNA expression of inflammatory mediators and the disease activity parameters of these patients. Moreover, Sema3B, Sema3C, Sema3F and Sema3G mRNA expression was significantly lower in early arthritis patients who developed persistent disease compared with patients with self-limiting disease after two year follow-up. Sema3F and Sema3B expression was significantly lower in patients that developed RA after 2 years of follow-up compared to those who remained as undifferentiated arthritis patients. FLS expression of Sema3A was significantly induced after IL-1, TNF or LPS stimulation, while the expression of Sema3B and Sema3F was down-regulated. Finally, functional assays showed that Sema3A significantly induced the migration and invasion of FLS. In contrast, Sema3B and Sema3F reduced spontaneous FLS migration and PDGF-induced cell invasion. Conclusion our data demonstrate that class 3 semaphorins are differentially expressed in the synovium of early patients depending on the severity and the progression of the disease and that Sema3A, Sema3B and Sema3F play an important role in the invasive capacity of RA FLS. Together, class 3 semaphorins and their receptors could be useful biomarkers and promising therapeutic targets for the treatment of RA.