Three transgenic sugarcane populations produced by Agrobacterium tumefaciens infection were analysed for the presence of genomic variability. Plants of the original cultivar, plants regenerated without transformation, as well as transformed and untransformed calli were used as control treatments. Amplified fragment length polymorphism (AFLP) of DNA extracted from leaves or calli assessed genomic profiling. The average DNA polymorphism within each population was determined by calculating the polymorphism index, while the extent of genomic dissimilarity among individual plants within transgenic populations was verified in unweighted pair group method using arithmetic averages dendrograms. The results showed that the production of transgenic sugarcane plants by A. tumefaciens infection is accompanied by limited but detectable genomic changes and that, on average, these occur at the same rate in plant populations carrying different transgenes. Main factors contributing to somaclonal variation in transgenic sugarcane plants have been verified by pre-existing DNA polymorphism into the donor genotype and in vitro culture steps during the transformation procedure. The relevant practical conclusion from this finding is that the AFLP analysis may be effectively used to identify individual transgenic plants with the least genomic deviation from the parental ones. The selected genotype would be conserved as cultivated sugarcane is asexually propagated.