Endothelium-dependent relaxations were studied in the thoracic aorta (TA) of the C57BL/6J mouse, a strain used commonly in the generation of genetically altered mice, to clarify some methodological questions. First, we have tested if transcardial perfusion with heparinized Krebs solution before the preparation of the TA may improve in vitro relaxant responses. Carbachol, thrombin, and ATP induced significantly stronger relaxations in TAs prepared from perfused animals than in controls. The effect of sodium nitroprusside (SNP), however, did not change, indicating that the improvement of the endothelium-dependent relaxations after perfusion was not caused by increased reactivity of the vascular smooth muscle to NO. Second, the potential regional differences within the TA were studied. Carbachol relaxed significantly stronger distal than proximal TA segments, whereas the effects of thrombin, ATP, and SNP showed no regional heterogeneity. Third, the relaxant effect of carbachol was partially preserved in TAs of endothelial NOS deficient (eNOS-/-) animals and remained unchanged in the presence of indomethacin, indicating the involvement of an eNOS- and cyclooxygenase-independent mechanism in the mediation of the response. Thrombin and ATP were ineffective in eNOS-/- TAs. Finally, TAs prepared from mice housed in cages equipped with running wheels did not show improved reactivity, indicating that the conventional housing conditions and the consequent sedentary lifestyle of the laboratory mouse do not diminish endothelial function in the TA.