Background Following a craniotomy, harvested bone flap, if available, is stored for future cranioplasty. There are two different methods for bone banking: subcutaneous pocket in abdominal wall and cryopreservation in a refrigerator. This study is designed to evaluate risk of developing infection in each group, retrospectively. Methods In this prospective observational multi-center study, one hundred (100) patients who underwent cranioplasty with autologous bone flap were divided into two groups of 50 patients. rate of clinical post-operative infection and possible associated risk factors were analyzed with statistical measures. The data check lists parameters were indication of DC, CP vs SP, interval between craniotomy and cranioplasty, post-operative hospitalization duration, new morbidities and possible mortalities. The data were analyzed by an expert bio-statistician with proper bio-statistical methods (p<0.05) Results Four (4) patient in cryopreservation group (50 patients) had post-operative bone flap infection (8%).in subcutaneous pocket method no post-operative infection after cranioplasty was noticed, which are not statistically significant (p=0.054). over-all post-operative infection rate was 4%. Conclusion There were no significant differences in post-operative infection rate between cryopreservation versus subcutaneous pocket method in storing bone flaps. Older age maybe associated with infection development after cranioplasty.