Assessment of systemic and regional hemodynamic phenotypes in genetically engineered mice by nonradioactive methods is yet an unsolved problem. We therefore investigated whether the reference sample method using fluorescent microspheres (FMs), already validated in rats, might be used for this purpose in C57BL/6 and in apolipoprotein E (ApoE)-deficient mice. FMs were injected into the left ventricle of instrumented anesthetized mice. In 10-week-old C57BL/6, cardiac output was 18-19 ml/min, and its regional distribution under basal conditions was similar to 1.5% (brain), 3.5% (heart), 9.1% (left kidney), 9.8% (right kidney), 1% (spleen), and 0.8% (stomach) (i.e., values similar to those previously reported with radioactive microspheres). Proper mixing of FMs was achieved as both kidneys had identical flows; distribution of two differently labeled FMs injected simultaneously was shown to be identical by an agreement study, and FM trapping in the capillary bed was demonstrated both histologically and by the recovery in the lungs of 90% of intravenously injected FMs. In addition, identical values for cardiac output and its distribution were obtained in different age-matched groups of C57BL/6. The FM technique also proved to be able to evidence angiotensin II and isoprenaline classic systemic and regional hemodynamic effects. Finally, applied to 30-week-old ApoE-deficient mice and age-matched C57BL/6, the FM technique showed no major hemodynamic difference between the two groups, except for coronary blood flow, which was significantly decreased in ApoE-deficient mice. In conclusion, we demonstrated for the first time the feasibility, accuracy, and reliability of the FM technique at characterizing the cardiovascular phenotype of genetically engineered mice.