In order to clarify the physiological effects of Chlorella intake on subjects with high-risk factors for lifestyle-related diseases, we conducted Chlorella ingestion tests on 17 subjects with high-risk factors for lifestyle-related diseases and 17 healthy subjects over a 16-week period, including a 4-week post-observation period. We conducted blood biochemical tests and analyzed gene expression profile in whole blood cells in the peripheral blood before and after Chlorella intake. We confirmed that in both groups, Chlorella intake resulted in noticeable reductions in body fat percentage, serum total cholesterol, and fasting blood glucose levels. Through gene expression analysis, we found that gene expression profiles varied with Chlorella intake and identified many genes that exhibited behavior such that after the completion of the intake period, expression levels returned to pre-intake expression ones. Among these were genes related to signal transduction molecules, metabolic enzymes, receptors, transporters, and cytokines. A difference in expression level was found between the two groups at the start of the tests, and we were able to identify genes with noticeable variance in expression level resulting from Chlorella intake in the high-risk factor group. These included genes involved in fat metabolism and insulin signaling pathways, which suggests that these pathways could be physiologically affected by Chlorella intake. There were clear variations in the expression profiles of genes directly related to uptake of glucose resulting from Chlorella intake, indicating that the activation of insulin signaling pathways could be the reason for the hypoglycemic effects of Chlorella.