TEs account for a large fraction of the genetic variation found in crops. Numerous studies have reported examples of TE insertions regulating agronomic traits, usually by altering transcriptional levels of nearby genes. TEs have been recently active in rice (Oryza sativa), and young insertions are known to contribute to genetic and phenotypic variability. Nevertheless, the role that TE standing variation present in the rice ancestors (O. rufipogon and O. nivara) has played during rice domestication and breeding is unknown. In this study, we detected TE polymorphisms (TIPs) in a population of rice and their wild relatives (n = 290 accessions). We looked for TIPs linked to gene expression variation by performing TIP-eQTL mapping using transcriptomic data of the rice (indica and japonica) accessions. We found 829 TIPs associated with expression changes in cis (5Kb cut-off distance from gene). These insertions were enriched in promoter regions and often explained more transcriptional variance than SNP-eQTLs, suggesting that they could frequently be the causal mutation. Up to 66% of these TIPs were found in the population of wild relatives (n = 82 accessions), suggesting that they were present in the rice recent ancestor. Further analyses of the TIP-eQTLs revealed that they often affect genes related with domestication traits and had undergone differential patterns of selection on indica and japonica subspecies. Our results suggest that TE insertions inducing expression changes on signal transduction genes have been maintained in wild rice populations and have been selected during the domestication and adaptation of rice populations