Background: Boys with cryptorchidism are susceptible to infertility. However, there are few known molecular markers of cryptorchidism-related infertility. Potential genes and molecular pathways to drive cryptorchidism-related infertility were investigated in this study via bioinformatics methods.Methods: Gene Expression Omnibus (GEO) database was utilized to download raw GSE25518 (training set) and GSE16191 (validation set) datasets. GSE25518 was used for differentially expressed genes (DEGs) identification and weighted gene co-expression network analysis (WGCNA). Hub genes were identified from the intersection of key genes from DEGs and the key module in WGCNA. Hub genes’ expression differences and diagnostic value were subsequently verified via GSE16191. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Gene set enrichment analysis (GSEA) were deployed for functional annotation.Results: 761 definitive DEGs were identified while 12 hub genes (CHRM4, CCR4, LMNB1, MTNR1B, TAC3, TRHR, RAD54L, CCNA1, SMC1B, GPRC6A, SYCE2, TAS2R19) were identified finally. The hub genes were also differentially expressed and showed excellent diagnostic value to distinguish cryptorchidism from normal testes in GSE16191. Additionally, they were well correlated with genes from the hallmark_spermatogenesis gene set. And they might be involved in oxidative phosphorylation, MYC targets V1, cholesterol homeostasis, KRAS activation, etc. Hallmark_spermatogenesis gene set was significantly enriched by five hub genes (RAD54L, CCNA1, SMC1B, TAC3, MTNR1B).Conclusion: We have identified 12 genes that might become new biomarkers for cryptorchidism-related infertility while five genes (RAD54L, CCNA1, SMC1B, TAC3, MTNR1B) deserve more attention.