Peripheral quantitative computed tomography (pQCT) was used to determine percent body fat in mice, and relative liver fat in lemmings fasted for 0, 6, 12 or 18 hours to induce a wide range of liver fat content. Accuracy of the pQCT was determined by comparing pQCT-derived fat to that from chemical extraction using 30 male mice (whole body) and 26 female lemmings (liver only). To determine whether pQCT could measure changes in liver fat (%) in live animals, two groups of lemmings were scanned on 4 consecutive days under anesthesia. Controls (n = 3) had ad libitum access to food, whereas the fasted group (n = 5) was deprived of food for 18 hr before being measured on day 2 and then refed. The coefficient of variation (CV) for determining percent body fat in mice using the pQCT was 3.9% (±1.8 SD). Percent body fat determined by pQCT significantly overestimated percent fat as measured by chemical extraction (14.5 ± 3.2 vs 12.3 ± 2.9% respectively, P < 0.01, mean ± SD). However, percent body fat by pQCT was highly related to chemical extraction percent fat (r = 0.95, P < 0.001). The liver attenuation values from pQCT were highly related to percent liver fat (r=0.98, P<0.001) in lemmings. The technique showed excellent precision with a CV of 0.3 ± 0.1%. The two groups (control vs fasted) did not differ in their percent liver fat on day 1 (5.4% vs 5.8%). On day 2 the fasted group had a significantly higher percent liver fat than controls (5.9% vs 17.3%; p<0.05). Following refeeding, there were no significant group differences in percent liver fat on days 3 and 4. Our data indicate that pQCT has good accuracy and precision for determining percent body fat, and liver fat in small animals and can be used to track changes in liver fat over time.