Background: Our aim was to determinate bone mineral density (BMD), levels of biochemical markers and cytokines in children with chronic hepatitis B treated with interferon (IFN)-alpha and to investigate effect of IFN-alpha therapy on these variables. To the best of our knowledge, this is first study carried out about BMD and cytokine levels in pediatric patients with chronic hepatitis B treated with IFN-alpha. Methods: BMD, levels of parathyroid hormone (PTH), osteocalcin, C-terminal cross-linking telopeptide of type I collagen (CTX), calcium, alkaline phosphates ( ALP), cytokines as TNF-alpha, interleukin (IL)-1(beta), IL-2r, IL-6, and IL-8 were studied in 54 children with chronic hepatitis B (4 - 15 years old) treated with interferon alone (n = 19) or in combination with lamivudine ( n = 35) for six months and as controls in 50 age-matched healthy children. Results: There was no significant difference in respect to serum IL-1(beta), TNF-alpha and osteocalcin levels while serum IL-2r ( p = 0.002), IL- 6 ( p = 0.001), IL- 8 ( p = 0.013), PTH ( p = 0.029), and CTX ( p = 0.021) levels were higher in children with chronic hepatitis B than in healthy controls. BMD of femur neck ( p = 0.012) and trochanter ( p = 0.046) in patients were higher than in healthy controls. There was a statistically significant correlation between serum IL-1(beta) and osteocalcin ( r = - 0.355, p < 0.01); between serum IL-8 and CTX levels ( r = 0.372, p = 0.01), and ALP ( r = 0.361, p = 0.01); between serum ALP and femur neck BMD ( r = 0.303, p = 0.05), and trochanter BMD ( r = 0.365, p = 0.01); between spine BMD and IL- 2R ( r = - 0.330, p < 0.05). Conclusion: In conclusion, our study suggest that BMD of femur, serum IL- 2r, IL- 6, IL- 8, PTH, and CTX levels were higher in children with chronic hepatitis B treated with IFN-alpha alone or combination with lamivudine than in healthy children. High femur BMD measurements found in patients may suggest that IFN-alpha therapy in children with chronic hepatitis B could contribute indirectly to prevent from hip osteoporosis. Additionally, further investigations on effects of IFN-alpha for bone structure in children should be performed in the future.