Opiate-induced alterations in the gene expression of the opioid propeptides prodynorphin (PDYN) and proenkephalin (PENK) in the brain have previously been described. However, there are no studies examining opioid propeptide system alterations due to long-lasting heroin self-administration. In our study, using in situ hybridization, we measured PDYN and PENK mRNA levels in the dorsal striatum, central nucleus of amygdala (CEA), and nucleus accumbens (NAcc) shell and core in rats after 6 weeks of heroin self-administration (fixed ratio 5, 0.02 mg/kg/infusion of heroin i.v.) and their respective saline or heroin “yoked” control. Our results show an increase in the PDYN mRNA level in the CEA and NAcc shell and no changes of PENK gene expression after heroin self-administration. In addition, to dissociate pharmacological effects of heroin from those produced by motivational processes driving active heroin intake on the PDYN and PENK gene expression, we compared effects of response-dependent (contingent) and response-independent (noncontingent — “yoked” heroin control) heroin administration. We found no differences between contingent and noncontingent groups of rats. In conclusion, our results indicate neuroadaptations in the PDYN but not PENK gene expression in rat limbic forebrain during heroin self-administration. We show that such changes depend on direct pharmacological actions of heroin rather than contingent heroin intake. These neuroalterations probably occur as an adaptation to long-lasting heroin exposure and may underlie changes leading to compulsive drug use and addiction.