Pediatric oncologic patients often need parenteral nutrition (PN) during chemotherapy. Long-term use of soybean-based lipid emulsions is associated with progressive liver disease and cholestasis, whereas fish-oil based emulsions have anticholestatic effects. We studied the potentially hepato-protective effects of short-term use of SMOF lipids in children undergoing chemotherapy. Fifteen pediatric oncologic patients treated with SMOF lipids were retrospectively analyzed in respect to bilirubin and liver parameters and compared to matched-controls who had received soybean-based fat emulsions. For statistics the time-points baseline, Day 14 of PN (PN14), and post (Day+7) were chosen. None of the study patients developed cholestasis. Within the SMOF-lipid group there were no differences in the laboratory parameters between baseline, PN14, and post. In the control group, gamma glutamyltransferase (γGT) levels increased during PN (baseline vs. PN14, 26.43 vs. 63.00 U/l, P < 0.05). Lactate dehydrogenase (LDH) levels showed a significantly different behavior in the 2 groups: In the SMOF lipids group, LDH decreased whereas it increased in the controls (-32.75 U/l vs. + 29.57 U/l, P < 0.05). An advantage of fish oil-based fat emulsions can be shown even after short-term PN. In children undergoing chemotherapy the use of soybean-based fat emulsions but not SMOF lipids led to increased γGT levels.