Japanese Black cattle occasionally demonstrate growth retardation despite sufficient nutrient intake. To clarify hormonal and transcriptional characteristics, we investigated differences in blood components, including hormones, and differences in exhaustive gene expressions in the liver and peripheral lymphocytes of six cattle with growth retardation (GR cattle) and eight control cattle of the same age and pedigree with normal growth. Hematocrit values and concentrations of hemoglobin, serum albumin, total cholesterol, insulin-like growth factor 1 (IGF-1), thyroxine and insulin in GR cattle were significantly lower than those in controls. GR cattle also excreted higher levels of GH. We used three GR and three control cattle for a microarray analysis in the liver and found that 279 gene expressions were significantly different. However, gene expressions related to the GH-IGF-1 axis, such as the GH receptor and IGF-1, were not significantly different from those of controls. Immune-related gene expressions were significantly lower. To clarify these gene expression levels, peripheral lymphocytes were used for real-time RT-PCR. The expression rates of genes that were significantly lower in the liver, such as chemokine ligand 8, interferon gamma receptor 1 and immunoglobulin light chain VJ region were also significantly lower in three GR cattle than those in the three control cattle. These results suggest that the cause of growth retardation in the present study was due to other factors, not abnormal gene expressions of factors related to the GH-IGF-1 axis in the liver, and that GR cattle were susceptible to infectious disease.