Tuberosity grafts had a greater percentage of lamina propria and lower percentage of submucosa when compared to lateral palate grafts. The study aims to understand the differences in the structural composition of soft tissue autografts harvested from the lateral palate or the tuberosity. Patients were randomly allocated to receive autografts harvested either from palatal or tuberosity sites to augment horizontal volume deficiencies around single-tooth implants. Tissue biopsies were analyzed for histological and histo-morphometric analysis. Picro-sirius red stain was used to evaluate collagen 1 and 3. Also, immuno-histochemical analysis was performed against MMP1, MMP2, cytokeratin-10, cytokeratin-13, and lysine hydroxylase-2. Twenty specimens were harvested from 9 subjects in the lateral palate group (PG) and 11 subjects in the tuberosity group (TG). The percentage of lamina propria represented 51.08% in the PG group and 72.79% in the TG group, while the area of submucosa was minimal in the TG group representing 4.89% of the total sample vs 25.75% in the PG. The total area of COL-1 and 3 in the TG was 1.19 ± 0.57 and 0.72 ± 0.44 mm2, respectively, while in the PG, the corresponding values were 1.4 ± 0.7 and 1.04 ± 0.5 mm2. The immuno-histochemical analysis generally showed a higher expression of LLH-2, MMP2, CYT-10, and CYT-13 in the TG when compared with the PG. Tuberosity grafts had a greater percentage of lamina propria and lower percentage of submucosa. The collagen content in the lamina propria was similar for both groups while the immuno-histochemical profile showed differences in the antibody expression of the epithelial cells. Tuberosity grafts had more lamina propria and less submocusa, which may be beneficial for volume augmentation.