In this study, the relationship between the expression of 5-HT2A receptors and level of 5-HT2A receptor mRNA in discrete regions of rat brain was examined by inactivating 5-HT2A receptors with the alkylating agent N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (EEDQ; 10 mg/kg, i.p.) and measuring the time course of receptor recovery and changes in mRNA levels. In untreated controls, the distribution and levels of 5-HT2A receptors labeled with [3H]ketanserin and receptor mRNA labeled with a 230-base 33P-labeled riboprobe were found to be highly correlated in most sub-regions of the cortex, the caudate-putamen and the claustrum but not in the piriform cortex or the hippocampus. Administration of EEDQ produced 90-99% inactivation of 5-HT2A receptors and the rate of receptor recovery was uniform in most regions studied. 5-HT2A receptors in most regions reached control levels by day 14, the lone exception being the caudate-putamen where receptors reached only 56% of control by day 14. Following inactivation of receptors with EEDQ there was a transient increase in levels of 5-HT2A receptor mRNA in several regions. Although rates of receptor recovery were uniform, four distinct patterns of mRNA response were observed: (1) early elevation followed by late elevation, (2) early elevation only, (3) late elevation only, and (4) no detectable change. The absence of a direct relationship between changes in 5-HT2A receptor mRNA and 5-HT2A receptor recovery in this model system suggests that transcriptional regulation is not the mechanism controlling the recovery of these receptors after irreversible inactivation. This study also lends support to the idea that alternative mechanisms may play a role in 5-HT2A receptor regulation after other pharmacological and physiological manipulations. The regional variability in 5-HT2A mRNA regulation reported here highlights the importance of using techniques with a high level of anatomical resolution to study changes in 5-HT2A receptor mRNA levels.