Background: Familial Mediterranean fever (FMF) has episodic or subclinical inflammation that may lead to a decrease in bone mineral density (BMD). The objective of this study was to assess BMD in Egyptian children with FMF on genetic basis.Methods: A cross sectional study included 45 FMF patients and 25 control children of both sexes in the age range between 3-16 years old. The patients were reclassified into two groups, namely group I(A) with 23 cases using colchicine for 1 month or less, and group I(B) with 22 cases using colchicine for more than 6 months. For both the patients and control groups, MEFV mutations were defined using molecular genetics technique and BMD was measured by DXA at the proximal femur and lumbar spines.Results: Four frequent gene mutations were found in the patient group E148Q (35.6%), V726A (33.3%), M680I (28.9%), and M694V (2.2%). There were also four heterozygous gene mutations in 40% of the control children. Patients receiving colchicine treatment for less than 1 month had highly significant lower values of BMD at the femur and lumbar spines than the control children (P=0.007, p <0.001). Patients receiving colchicine treatment for more than 6 months had improved values of BMD at femur compared with the control, but there were still significant differences between them in lumbar spine (P=0.036). There were insignificant effect of gene mutation type on BMD and the risk of osteopenia among the patients.Conclusion: FMF had a significant effect on BMD. However, regular use of colchicine treatment improves this effect mainly at the femur.