Herbicide application in the fruit tree nursery as an element of good agrotechnical practice quite often might be risky for the appearance of phytotoxic symptoms in plants. That is why preliminary studies are needed to estimate the effect of different herbicides on the vegetative habits of the rootstocks. The aim of the present research was to study the effect of the soil herbicides Terbacil, Pendimethalin and Napropamide on isolated Prunus cerasifera embryos and some micropropagated rootstocks for fruit species - GF677, ÌÌ106 and Prunus domestica “Wangenheims” under in vitro conditions. Inhibition of root meristem growth and browning of cotyledons were established after the treatment with pendimethalin of Prunus embryos with embryonic roots shorter than 5mm. The soil herbicides terbacil, pendimethalin and napropamid caused phytotoxicity expressed in suppression of the root growth of rooted plants of GF677 under in vitro conditions. Visual symptoms of phytotoxicity in the leaves and stems were not established. Pendimethalin and napropamid depressed the stem and root growth of the apple rootstock MM106 plantlets. After treatment with terbacil of in vitro rooted “Wangenheims” plants no external symptoms of phytotoxicity – chlorosis, necrosis and depressing effect were observed. After treatment with pendimethalin and napropamide, a depressing effect on the root formation and growth of microplants without roots were established. The applied herbicides blocked rooting of Prunus domestica “Wangenheims” under in vitro conditions.