Response of callus of three apple (Malus domestica, Borkh) cultivars (cv.) namely: Balady, MM 106 and MM 111 were investigated under different concentrations of silicon nanoparticles (Si-NPs) (0, 10 and 100 mgl^-1) and salt stress, induced by NaCl (0, 2000 and 4000 ppm). At non-salt stressed conditions, the highest values of fresh weight (FW) of callus were obtained with addition of 4 mgl^-1 of 2,4-D with Kin at 0.4 mgl^-1 to MS medium for all cvs. FW was increased by more than 80% after application of 10 and 100 mg/l of Si-NPs in Balady and MM111 cvs., respectively under 2000 ppm of NaCl. Anatomically, the maximum polar and equatorial diameters (72 and 53µm, respectively), of callus cells were observed in MM111cv. under high salinity level. Also, 7 amplicons amplified with three different SCoT primers (SCoT 77, 66 and 26) in both salt stressed and unstressed callus in MM111cv.  Addition of Si-NPs increased the total antioxidants (%), the activity of peroxidase (POD) and superoxide dismutase (SOD) in salt stressed callus in all cvs. Application of high Si-NPs concentration increased the POD and SOD activity by 6.5 and 5.7 times, respectively in Ballady cv. under high NaCl levels. Also, high concentration of free amino acids, proline, reducing sugars and free phenolics concentration were observed in salt stressed callus with increment the concentration of Si-NPs. Proline and reducing sugars concentrations were increased by 80% in salt-stressed callus of Ballady cv. under 100 mgl- of Si-NPs. It can recommend that, application of Si-NPs at 10 mgl^-1 will increase the tolerance of apple callus to 2000 ppm NaCl, especially in Balady and MM111 cvs, as a suitable salt tolerant rootstock for apple grafting.