BACKGROUND: Autophagy was a significant catabolic process which played a critical role in the maintenance of cellular homeostasis and viability in a stressed state. The dysregulation of autophagy was correlated with various diseases. The aim of our study was to develop a prognostic signature for papillary renal cell carcinoma (RCC). METHODS: First, 40 differently expressed genes related with autophagy (ARGs) were examined via high-throughput sequencing and large-scale databases. Then, functional enrichment analysis was performed to explore the biological attributes of these ARGs. The Cox proportional hazard regression hinted that four ARGs (P4HB, BIRC5, NGR1 and PRKN) were significantly correlated with overall survival (OS). Thus, we got genes with prognostic value. Finally, a prognostic index (PI) was constructed. RESULTS: After identifying the 4 ARGs, we profiled our risk signature. Based on the PI we developed, papillary RCC patients were stratified into high-risk and low-risk groups. High-risk patients had significant shorter OS than low-risk patients (P