Background/Aims: Lipid metabolic disarray in the liver of young and adult mice offspring is induced by saturated fatty acids (SFA) but prevented by α-linolenic acid (ALA, 18:3 ω-3) in the maternal diet during pregnancy and lactation. The aim of the present study was to analyze the impact of maternal dietary ALA compared to an SFA diet on the liver gene expression in the newborn offspring. Methods: C57Bl6/J dams were fed with diets normal in calories but rich in ALA or SFA before mating and during pregnancy. Pups were sacrificed at birth and liver parameters were assessed. Gene expression was characterized by microarray analysis and validated by real-time quantitative PCR. Results: ALA, compared to SFA, in maternal diets during pregnancy increased polyunsaturated fatty acids, while it differentially modified fatty acid desaturase activities in offspring liver. Overall, 474 and 662 genes from the liver of newborn pups were differentially regulated by ALA and SFA compared to control diet (p < 0.05; fold change 2), respectively. Notably, Per3 was upregulated by ALA, whereas it was downregulated by SFA, compared to control diet. Conclusions: ALA- and SFA-enriched diets differentially affect the gene expression pattern in the offspring's liver. ALA, in particular, upregulates genes associated with low adiposity.