Microarray transcriptome analyses of fetal mouse liver did not detect circadian expression rhythms of clock genes or clock-controlled genes, although some rhythmic transcripts that were likely not driven by endogenous cellular clocks were identified. This finding reveals a key distinction between the circadian oscillators in fetal and adult mouse livers. Thus, in this study, the transcriptomes of fetal and adult livers were systematically compared to identify differences in the gene expression profiles between these two developmental stages. Approximately 1000 transcripts were differentially enriched between the fetal and adult livers. These transcripts represent genes with cellular functions characteristic of distinct developmental stages. Clock genes were also differentially expressed between the fetal and adult livers. Developmental differences in liver gene expression might have contributed to the differences in oscillation status and functional states of the cellular circadian clock between fetal and adult livers.