Mice that lack or over-express a gene of interest are important tools for unraveling gene function. The determination of single nephron function by micropuncture or precise determination of glomerular filtration rate (GFR) by inulin clearance method require experiments under anesthesia. A good anesthetic protocol should allow for reasonable and stable glomerular and tubular function. The aim of this study was to compare the commonly used thiobutabarbital (TBB) versus alpha-chloralose (CHL) anesthesia with regard to absolute levels and the stability of blood pressure, heart rate, and kidney function. Male CD1 mice were anesthetized with TBB (100 mg/kg body weight i.p.) or CHL (120 mg/kg body weight i.p.), plus ketamine (100 mg/kg body weight i.m.) given to every mouse for analgesia. After preparation for clearance experiments, two 30-min urine collections were performed at periods 1 and 2 (P1 and P2). It was observed that heart rate and mean arterial blood pressure did not differ between TBB ( n=9) vs. CHL ( n=9) and were stable through P1 and P2. In CHL, GFR as well as fractional excretion of fluid, Na(+) and K(+) were stable from P1 to P2 (P1: 190+/-15 microl/min, 1.6+/-0.2%, 0.7+/-0.1%, 35+/-5%; percent change in P2: 1+/-6, 26+/-10, 29+/-15, 6+/-10 respectively). In TBB, GFR was significantly greater vs. CHL in P1 and did not significantly change in P2 (246+/-8 microl/min, p<0.05; percent change: -6.5+/-4). Fractional excretion of fluid, Na(+) and K(+) were not significantly different vs. CHL in P1, but significantly increased in P2 (P1: 1.5+/-0.2%, 1.1+/-0.2%, 31+/-3%; percent change in P2: 122+/-23, 128+/-21 and 29+/-6 respectively; each p<0.05 vs. P1). In conclusion, mice under both anesthetic regimens present reasonable and stable blood pressure and reasonable kidney function, but kidney reabsorption is more stable under CHL than under TBB anesthesia, which may facilitate study of the response in kidney function to acute interventions.