Paraquat is a fast-acting non-selective herbicide widely used globally to eradicate weeds. The emergence of weed resistance has fueled the drive to understand molecular mechanistic aspects and develop crops resistant to the herbicide. The transport of paraquat is mediated by members of the L-amino acid transporter family and are prime targets for the development of resistance. However, these transporters also facilitate the transport of natural essential molecules such as polyamines and thiamine (vitamin B1), at least in Arabidopsis, but have not undergone rigorous investigation in crops. Here we report on disruption of the polyamine transporter PUT3 in two japonica rice cultivars. Both rice put3-mutant alleles are resistant to paraquat and display low percentage germination concomitant with altered polyamine profiles whereas thiamine is unchanged. Notwithstanding, seedlings that germinate behave like wild type in the Tainung 67 cultivar, whereas further growth and development is strongly impaired by disruption of PUT3 in the Hwayoung cultivar. The growth phenotype could be complemented by ectopic expression of PUT3, which also restores the polyamine profile thus linking the defects to disruption of the gene. Our study provides biological insight into the divergent characteristics of rice cultivar tissues as a function of their polyamine profile and a warning to exercise caution upon disruption of transporters to facilitate paraquat resistance in crops as this may also lead to severe fitness penalties.