Objective To evaluate the comparability of test results of human serum AFP and β-hCG by two instruments. Methods The serum samples collected from 198 pregnant women with 15～20 weeks and 3 batches of control serum were divided into two group randomly. One group samples were detected with Roche cobas e601 chemiluminescent immunoassay analyzer, the other group with Beckman Coulter Accesss DXI800. The comparison of high risk of Down’s syndrome (DS) and neural tube defects (NTD) between two instruments were carried out. Results There was obvious significance on detection of serum AFP and β-hCG levels between two instruments (P＜0.05). It was verified by different levels of quality control materials bias within the scope of the permit. Five cases of DS high-risk and four cases of NTD high risk in 198 serum samples were all detected by two instruments without significant difference between them (P=1.000). Conclusion The results of prenatal screening by two instruments meet the clinical requirements.