Complex comminuted fractures are accompanied by development of bone defects and loss of reparative potential of the bone tissue in the region of the trauma. This brings the necessity of using implants with optimum osteoconductive and osteointegration properties. The objective of the study was determining the condition of biochemical bone markers and peculiarities of histomorphological changes under the influence of ceramic hydroxyapatite (HA) implants with various physical-chemical properties in the conditions of diaphyseal bone defects in rabbits. We composed control and experimental groups of rabbits with 10 individuals in each with diaphyseal bone defects (3 mm) of the radial bones formed under general anesthesia. In one experimental group, they were filled with granules of hydroxyapatite with α-tricalcium phosphate, and in the second group – with β-tricalcium phosphate, alloyed with Si. In the control rabbits, the defects healed under a blood clot. Blood was analyzed on the 3rd, 7th, 14th, 21st and 42nd days, and as reference we used biochemical parameters of blood of clinically healthy rabbits (n = 10). Bone biopsied materials were taken on days 21–42 under general anesthesia. When using hydroxyapatite with β-tricalcium phosphate, alloyed with Si, we determined early intensification of the levels of nitrogen oxide, angiogenesis and development of bone regenerate in conditions of shortening of inflammatory resorption phase, which was verified according to the level of tartrate-resistant acid phosphatase. According to the level of bone isoenzyme of alkaline phosphatase in the blood serum of animals of the control group, the reparative osteogenesis developed slowly and peaked on day 42, whereas in animals implanted with α-tricalcium phosphate, its development peaked peaked on days 14–42, and when using Si-alloy – on days 7–14. Histomorphologically, on the 21st day, in the case of replacement of bone defect with hydroxyapatite with α-tricalcium phosphate, coarse-fibered type of bone regenerate developed with no dense contact with the elements of the regenerate, while spongy bone trabeculae occurred when hydroxyapatite was applied with β-tricalcium phosphate alloyed with Si, and the control rabbits were observed to be in the stage of cartilaginous callus. On the 42nd day, under the influence of implants of hydroxyapatite with α-tricalcium phosphate, the spongy bone tissue transformed into compact tissue with further mineralization. With implants alloyed with Si, there occurred compact bone tissue, and bone regenerates of the control animals were regions of coarse-fibered and spongy bone tissue without dense contact with the parent bone. This study revealed that hydroxyapatite with β-tricalcium phosphate alloyed with Si had notable osteoinductive and osteointegrating properties, as indicated by early angiogenesis and osteoblast reaction, positive dynamics of the marker biochemical parameters with faster and better development of bone regenerate as spongy bone trabeculae.