Many of the most modern drugs are of a protein nature and are synthesized by transgenic producer organisms. Bacteria, yeast, or animal cell cultures are commonly used, but plants have a number of advantages—minimal biomass unit cost, animal safety (plants are not attacked by mammalian pathogens), the agricultural scale of production, and the ability to produce complex proteins. A disadvantage of plants may be an unstable level of transgene expression, which depends on the transgene structure and its insertion site. We analyzed the structure of T‐DNA inserts in transgenic tobacco plants (Nicotiana tabacum L.) belonging to two lines obtained using the same genetic construct but demonstrating different biological activities of the recombinant protein (bovine interferon‐gamma). We found that, in one case, T‐DNA was integrated into genomic DNA in the region of centromeric repeats, and in the other, into a transcriptionally active region of the genome. It was also found that in one case, the insert has a clustered structure and consists of three copies. Thus, the structure of T‐DNA inserts in both lines is not optimal (the optimal structure includes a single copy of the insert located in the active region of the genome). It is desirable to carry out such studies at the early stages of transgenic plants selection.