The periodontal ligament (PDL), connective tissue located between the cementum of teeth and alveolar bone of the mandibula, plays a crucial role in the maintenance and regeneration of periodontal tissues. We previously reported that endoglin was involved in the bone morphogenetic protein (BMP)-2-induced osteogenic differentiation of mouse PDL cells, which is associated with Smad-2 phosphorylation but not Smad-1/5/8 phosphorylation. Further, we found that the BMP-2-induced Smad-2 phosphorylation was, at least in part, dependent upon endoglin. In this study, to elucidate the detailed mechanism underlying the BMP-2-induced signaling pathway unique to PDL cells, we performed a cDNA microarray analysis to identify endoglin-dependent BMP-2-responsive genes in PDL-L2, a mouse PDL-derived cell line. Here we provide experimental methods and obtained dataset to correspond with our data in Gene Expression Omnibus (GEO) Datasets.