Sex determination from skeletal remains is a principal step in any archeological or forensic study. This study aimed to evaluate the role of scapular and clavicular bones measurements for sex determination in Egyptian population sample using 3D CT images and to obtain function equation for sex differentiation. This was a cross sectional study conducted on 135 CT images (66 males and 69 females) obtained from Radiology Department, Menoufia University Hospital. Five measurements of scapula and three of clavicle bilaterally were measured. All scapular measurements of males were significantly of higher values than those of females (p < 0.001). Maximum scapular height (MSH) and scapular breadth (SB) had the highest accuracy on the right side (84% each) where on the left side, MSH had the highest accuracy followed by SB (84% and 81% respectively). Male clavicles were significantly longer and had higher sagittal (SCD) and vertical diameter (VCD) at mid-clavicular point than female ones. Right clavicular length had the highest accuracy followed by SCD (81.5% and 79.9% respectively). While the left SCD had the highest accuracy followed by the left clavicular length (82.5% and 81.5% respectively). Bilateral symmetry of scapular and clavicular bones was present. Sex equations formulae using logistic regression analysis were obtained for all measurements. Scapulae and clavicles were useful bones for sex determination in this Egyptian population sample. CT was a reliable and an accurate method for sex determination from these bones. Application of the recovered equations from the current research is recommended.