Since small-animal MRI generally requires anesthesia, the effect of the anesthetic regimen on the explored organ(s) has to be taken into account for study interpretation. In this work, we assess the influence of ketamine/xylazine and isoflurane anesthesia on left-ventricular (LV) function in the mouse in vivo by cine-MRI. Three groups of animals were anesthetized with ketamine/xylazine (n = 13) and two different concentrations of isoflurane (1.25%, n = 12 and 2.00%, n = 12) delivered in O2/N2O mix. Long- and short-axis cine-MRI was performed to measure end-diastolic volume, stroke volume, ejection fraction and LV wall thickness. Ketamine/xylazine significantly reduced heart rate, cardiac output and wall thickness, but increased stroke volume and end-diastolic volume compared with both isoflurane groups. No differences across all groups were observed in ejection fraction or systolic wall thickening. Breath rate under isoflurane was significantly lower and concentration dependent, whereas heart function was independent of concentration in all measured parameters. These findings are in agreement with echocardiography and catheterization studies. Isoflurane is advantageous for MR studies because it better maintains cardiac function. Taking into account previously obtained myocardial perfusion measurements, isoflurane concentration should, however, be maintained at the minimum required for a stable sleep even if cardiac function is unaffected by higher isoflurane concentrations.