This paper focuses on gene silencing, its role in developing transgenic plants and the various molecular mechanisms behind it. Particular emphasis is given on: transcriptional gene silencing; chromosomal environment of the transgene; repeat induced DNA methylation; DNA-DNA interaction; post-transcriptional silencing (PTGS); role of transgene expression level; PTGS and methylated transgenes; elimination of homologous transcripts (RNA-dependent RNA polymerase-complementary RNA model); and the number of transgenes per integration site.