Cocaine is an inhibitor of the dopamine, norepinephrine and serotonin reuptake transporters. Because its administration would elevate signaling of all these three neurotransmitters, many studies have been aimed at attributing individual effects of cocaine to specific transmitter systems. Using mice with a cocaine-insensitive dopamine transporter (DAT-CI mice), we previously showed that cocaine-induced dopamine elevations were necessary for its rewarding and stimulating effects. In this study, we observe that DAT-CI mice exhibit cocaine-conditioned place aversion (CPA), and that its expression depends on their genetic background. Specifically, DAT-CI mice backcrossed to the C57Bl/6J strain background did not display a preference or an aversion to cocaine, whereas DAT-CI mice that were on a mixed 129S1/SvImJ × C57Bl/6J (129B6) background had a robust CPA to cocaine. These results indicate that while inhibition of the DAT is necessary for cocaine reward, other cocaine targets and neurotransmitter systems may mediate the aversive properties of cocaine. Furthermore, the aversive effect of cocaine can be observed in the absence of a DAT-mediated rewarding effect, and it is affected by genomic differences between these two mouse strains.