Abstract: Objective To investigate the expressions and clinical significance of autophagy-related gene 2B （ATG2B），autophagy-related gene 4D （ATG4D） , autophagy-related gene 9B（ATG9B） in breast cancer cell lines and breast cancer. Methods Cancer Browser screening was applied to study the differential expressions ofATG2B, ATG4D, ATG9Bgenes in breast cancer. Quantitative Real-time PCR was used to measure the expressions of these three genes in human breast cancer cell lines (MCF-7, MDA-MB-231, MDA-MB-435S and ZR-75-30) as well as 83 cases of breast cancer samples with paired normal breast tissues. The relationships between the expressions of these genes and clinicopathological characteristics were further analyzed. Results Cancer Browser screening found abnormal expressions of ATG2B, ATG4D, ATG9Bin breast cancer （ P=0.015， P=0.028， P=0.040）. All four breast cancer cell lines expressed ATG2B, ATG4D, ATG9B,and the expression of ATG2B, ATG9B was significantly lower than positive control ( P<0.001), but ATG4D expression was higher than positive control ( P<0.001). The expressions of ATG2B, ATG4D, ATG9B in breast cancer were all lower than those in the adjacent normal tissues ( P<0.001, P=0.031, P<0.001). Furthermore, the expression of ATG2B was correlated with ER ( r =0.949， P=0.015), and the expression of ATG4D was related to age ( r =-0.449， P=0.005), the expression of ATG9B was correlated to lymph node metastasis and cytokeratin 5/6 status ( r =0.339， P=0.043; r =0.533， P=0.043). Conclusion ATG2B, ATG4D, ATG9Bgenes shows low expressions in breast cancer, which may become new molecular markers for the prognosis of breast cancer.