Genome-wide association study (GWAS) has identified serine/threonine kinase 39 (STK39) as a candidate gene for hypertension. A replication study provided supporting evidence that STK39 functional polymorphism rs35929607 was associated with hypertension. Recently, another study also showed rs6749447 within the STK39 was associated with blood pressure responses. However, these studies were all conducted in Caucasians. Thus, we carried out a case-control study to test whether STK39 is a common candidate gene for hypertension, and to examine the interaction of genetic factors and non-genetic risk factors in the Chinese population. Thousand twenty four hypertensive cases and 1024 controls were genotyped for five polymorphisms. Four single-nucleotide polymorphisms (SNPs) are located within STK39, and rs4977950, the SNP that showed the strongest signal is located in a gene desert. Results indicated that none of these SNPs was associated with hypertension in the Chinese population. Logistic regression analysis found body mass index (BMI) and triglyceride level were higher in the hypertension group when compared with the control group. Multifactor dimensionality reduction analysis indicated that the interaction between BMI and rs4977950 may have an impact on hypertension. Taken together, the present study found no evidence that STK39 was associated with hypertension in the Chinese population. Instead, non-genetic risk factors such as BMI have an important role in Chinese hypertensive subjects, and the 'missing inheritability' requires further investigation.