Amygdalin is most commonly occurring cyanogenic glycoside. It is found in seeds of many plant species. Our study was aimed to reveal whether pure intramuscularly injected amygdalin or apricot seeds peroral exposure cause changes in bone microstructure of rabbits. Twenty clinically healthy 5 months-old male rabbits were segregated into five groups. Animals from groups A1 and A2 were intramuscularly injected with amygdalin at doses of 0.6 and 3 mg/kg b.w. daily for 28 days. The groups S1 and S2 received commercial feed for rabbits mixed with crushed bitter apricot seeds at doses of 60 and 300 mg/kg b.w. during 28 days. The control (C) group did not receive any amygdalin. Intramuscular and peroral amygdalin administration did not affect total body weight, femoral length and femoral weight of rabbits. Similarly, microcomputed tomography (3D analysis) has shown that amygdalin had insignificant effect on relative bone volume, bone mineral density, cortical bone thickness, bone surface, trabecular thickness, trabecular number, trabecular separation. However, histological (2D analysis) revealed evident changes in compact bone microstructure of amygdalin-exposed rabbits consistent with a different vascularization and changed biomechanical properties. We can conclude that subacute exposure to amygdalin (both intramuscular and peroral) at the doses used in our study influenced compact bone remodeling.