AimsThe aim of this randomized controlled clinical trial was to compare the gene expression, micro‐CT, histomorphometrical analysis between biphasic calcium phosphate (BCP) of 70/30 ratio and deproteinized bovine bone mineral (DBBM) in sinus augmentation.Materials and MethodsTwenty‐four patients in need for sinus floor augmentation through lateral approach were randomized into BCP 70/30 ratio or DBBM. After at least 6 months of healing, a total of 24 bone specimens were collected from the entire height of the augmented bone at the area of implant placement and underwent micro‐CT, histomorphometric and gene expression analysis. The 12 bone specimens of BCP 70/30 ratio were equally allocated to micro‐CT and histologic analysis (test group, n = 6) and gene expression analysis (test group, n = 6). Similarly, the 12 bone specimens of DBBM were also allocated to micro‐CT and histologic analysis (control group, n = 6) and gene expression analysis (control group, n = 6). The newly formed bone, remaining graft materials and relative change in gene expression of four target genes were assessed.ResultsThe micro‐CT results showed no statistically significant difference in the ratio of bone volume to total volume (BV/TV ratio) for the two groups (BCP 41.51% vs. DBBM 40.97%) and the same was true for residual graft material to total volume (GV/TV ratio, BCP 9.97% vs. DBBM 14.41%). Similarly, no significant difference was shown in the histological analysis in terms of bone formation, (BCP 31.43% vs. DBBM was 30.09%) and residual graft area (DBBM 40.76% vs. BCP 45.06%). With regards to gene expression, the level of ALP was lower in both groups of bone grafted specimens compared with the native bone. On the contrary, the level of OSX, IL‐1B and TRAP was higher in augmented bone of both groups compared with the native bone. However, the relative difference in all gene expressions between BCP and DBBM group was not significant.ConclusionsThe BCP, HA/β‐TCP ratio of 70/30 presented similar histological and micro‐CT outcomes in terms of new bone formation and residual graft particles with DBBM. The gene expression analysis revealed different gene expression patterns between augmented and native bone, but showed no significant difference between the two biomaterials.