Aim: The Purpose of this study was to investigate the effects of bisphosphonate (Sodium alendronate) on root resorption of deciduous lower molars in rabbit.Materials and methods:This study was carried out using forty newborns healthy New Zealand white rabbits of average body weight 50-55 grams, their nutrition was provided maternally and a commercial pelleted diet of 16.7% crude protein, 13.7% crude fiber and 2590 kcal of digestible energy per kilogram would be added. The animals were classified into two main groups: Group1 (Control group): This group is consisted of 20 rabbits which were subjected to oral dose of 2.5 milligrams/kilogram of body weight/ day normal saline by using oropharengeal tube .The rabbits were divided in to two sub groups: Sub Group A: It is consisted of 10 animals, which were sacrificed by CO2 inhalation at the 10th day after birth. Sub Group B: It is consisted of 10 animals, which were sacrificed by CO2 inhalation at the 20th day after birth. Group 2 (BPS group):This group is consisted of 20 rabbits, which were subjected to daily oral dose of 2.5 milligrams/kilogram of body weight/ day sodium alendronate using oropharengeal tube [1] were divided into two subgroups: Sub Group A: It is consisted of 10 animals which were sacrificed by CO2 inhalation at the 10th day after birth. Sub Group B: It is consisted of 10 animals which were sacrificed by CO2 inhalation at the 20th day after birth. At the end of the experimental period; the mandibles were removed and hemisected. The hemisected mandibles were prepared for light microscope examination using hematoxyline and eosin (H&E) and tartrate resistant acid phosphatase (special histochemical stain). Results: I-Histological results: In control sub group A the deciduous molars of all animals have been fully erupted with considerable amounts of roots resorption. In control sub group B the deciduous molars of all animals have been completely shed.In Bps group subgroup A showed delayed eruption of the deciduous molars and some dental abnormalities . In Bps group subgroup B the deciduous molars still present with some degree of root resorption. Most of the crowns of the underlying premolars were formed with developing of their roots. Cementum-like tissue was found between the deciduous molars and erupting premolars .II-Histochemical results: The control sub group A showed large number of positively stained multinucleated odontoclasts on the resorbed dentin surface of deciduous molars with formation of Howship’s lacunae.The control sub group B showed negative stain in all layers of the erupting premolars (no odontoclasts were seen in this sub group).The Bps group subgroup A showed negative stain in all layers of the deciduous tooth germs that appeared in the late bell stage.The Bps group subgroup B showed negative stain in all layers of the erupting premolars as well as in all layers of the deciduous molars.Conclusions: Treatment with sodium alendronate (2.5mg/kg body wt. /day) from first day of birth resulted in delayed eruption of deciduous molars and some dental abnormalities as enlargements of predentin layer, discontinuity of odontobl astic layer, defective dentin mineralization and appearance of denticle-like structure in the pulp. TRAP histochemical results revealed that the treatment with Bps result in decrease numbers of odontoclasts and osteoclasts as their apoptosis and separation from Howship’s lacunae.