Communication technologies are moving toward higher microwave frequencies and bandwidths to satisfy the growing demand for high data rates. The concern about the possible effects of microwaves on plants and animals has increased recently. There is still uncertainty concerning the effects of microwaves on plants. The present study was conducted to investigate the effect of industrial, scientific and medical (ISM) radio band microwaves on seedlings and seeds of Arabidopsis thaliana (L.). In vitro growing A. thaliana wild-type seedlings and seeds were exposed to 2.45 GHz continuous-wave microwaves at a power flux density of 1.0 ± 0.1 W m −2 for 48 h. Microwave exposure increased the hydrogen peroxide content, photosynthetic pigments, nonphotochemical quenching and fluorescence of the seedlings, while peroxidase activity and F v /F m values were unchanged. Anthocyanin and malondialdehyde were decreased. Seed germination rate, fresh weight and photosynthetic pigment contents of 10-day-old seedlings obtained from microwaves exposed seeds remained unchanged. Results confirmed the inexistence of oxidative stress but a stimulatory effect of microwave on A. thaliana seedlings. The increased hydrogen peroxide content and nonphotochemical quenching suggest acceptance of extra photon energy and a portion of the excess captured photon passing through the photosystem, while a portion of energy dissipated as heat.