Introduction: The teratogenic effect of caffeine depends on the dosage and the route of administration. A daily oral dose of caffeine (80 mg/kg) is tetrogenic for rat. In present study, the teratogenic effects of caffeine on the development of bones and the resoption of skeletal cartilage in the rat embryo were quantitatively evaluation. Materials and Methods: Three groups of pregnant rats were used in the study, which were pregnant from the first time. The first experimental group received 175 mg/kg of 1% caffeine on the fourteenth day of the pregnancy, while the second experimental group received 80 mg/kg of 1% caffeine on days 14, 15 and 16 of the pregnancy. The third group was kept as control group. On day 20 and 21 of the pregnancy, the animal were sacrified and 209 embryo were collected which were used to evaluate the teratogenic effect of caffeine. The left caudal limbs of these embryo were cut, fixed, decalcifed, processed in paraffin, serially sectioned and stain with Hematoxyline and Eosin. The volumes of periosteum, perichondrium, trabecular bone, collar bone, whole and cartilage were calculated. A camera lucida was used for acquisition of the primary data. The analysis of the variance were used to compare the statistical difference among the parameters. Results: There were statistically significant reduction in all the parameters in the experimental groups as they were compared with the control group. No significant difference was noticed between the experimental groups. Conclusion: The injection of caffeine to pregnant rats causes a reduction in the extracellular bone matrix and delays the bone formation in their off spring.