Increase in aerobic glycolysis and mitochondrial dysfunction are important metabolic features in human cancers. However, it still remains unclear how these phenomena are developed during tumorigenesis. To maintain aerobic glycolysis, continuous generation of NAD+ by lactate dehydrogenase (LDH) with conversion of pyruvate to lactate is essential. Functional LDH is homo- or heterotetramers assembled from two types of subunit with LDHA and LDHB gene product. Recently, we reported that LDH5 isoenzyme formed by LDHB suppression is involved in increased glycolytic lactate production and mitochondrial respiratory defects in hepatoma cells. In this study, we aimed to investigate how LDHB suppression is linked with mitochondrial respiratory dysfunction. When LDHB expression was suppressed by siRNA-mediated knockdown, cellular oxygen consumption rate was significantly decreased without clear decrease in expressions of respiratory proteins. These results imply that LDHB suppression may control mitochondrial respiration through post translational modification or respiratory subunits or control of metabolites. Thus, we focused on pyruvate dehydrogenase (PDH) which is a key regulatory enzyme linking glycolysis and mitochondrial activity by controlling TCA cycle. Interestingly, LDHB knockdown effectively increased phosphorylation of PDH, indicating its inactivation. Treatment of lactate without LDHB knockdown increased PDH phosphorylation with lowering pH. This result implies that PDH phosphorylation is correlated with acidification, but is not lactate-specific event. Collectively, our results suggest that lactate-mediated PDH inactivation is the key mechanism to induce mitochondrial dysfunction in LDHB-suppressed hepatoma cell.