Fifty percent of Arabidopsis thaliana plants transgenic for a hygromycin resistance gene failed to transmit the resistance phenotype to the progeny. The complete transgene was, however, inherited in all cases according to Mendelian laws as observed by Southern analysis. This discrepancy between genotype and phenotype was the result of a reduced level of transcript in the sensitive transformants. The gene inactivation occurred in plants with multicopy integration of the foreign DNA. No definite correlation was found between gene inactivity and methylation of cytidine residues in the transgene sequence. Explants from several sensitive transformed plants regained a low level of hygromycin resistance on callus induction medium. Subsequent generations obtained by self-pollination were sensitive. In contrast, spontaneous restoration of hygromycin tolerance was observed in seedlings originating from out-crosses with wild-type plants or a different sensitive transformant. A reduction of the copy number was not a prerequisite for spontaneous reactivation. The resistance was often lost again in the next generation. Inactivation and reactivation of the transgene are therefore reversible.