The use of silver nanoparticles (AgNPs) in commercial products has increased significantly in recent years. However, findings on the toxic effects of the AgNPs are still limited. This paper reports an investigation on the cytotoxic and genotoxic potential of the AgNPs on root cells of Allium cepa. Germination (GI), root elongation (REI), mitotic (MI), nuclear abnormality (NAI), and micronucleus index (MNI) were determined for seeds exposed to various AgNPs diameters (10, 20, 51, and 73 nm) as well as to the silver bulk (AgBulk) (micrometer-size particles) at the concentration of 100 mg·L−1. Transmission electron microscopy (TEM) provided the particle size distribution, while dynamic light scattering (DLS) was used to get the hydrodynamic size, polydispersity index, and zeta potential of the AgNPs. Laser-induced breakdown spectroscopy (LIBS) and inductively coupled plasma/optical emission spectrometry (ICP OES) were applied for quantifying the AgNPs content uptake by roots. Silver dissolution was determined by dialysis experiment. Results showed that the AgNPs penetrated the roots, affecting MI, GI, NAI, and MNI in meristematic cells. Changes in these indicators were AgNPs diameter-dependent so that cytotoxic and genotoxic effects in Allium cepa increased with the reduction of the particle diameter. The results also revealed that the AgNPs were the main responsible for the cytotoxicity and genotoxicity since negligible silver dissolution was observed. Display omitted •Allium cepa seeds were exposed to different AgNPs dimensions (10, 20, 51, and 73 nm)•Cytotoxic and genotoxic effects of the AgNPs on root cells of the A. cepa were tested.•AgNPs were able to penetrate in plant cell and cause cell toxicity.•Cytotoxic and genotoxic effects increased with decreasing AgNPs diameter.•AgNPs were the main responsible for the toxicity.