We conducted a comprehensive study to investigate the role of genes involved in transport pathways in responseto chemotherapy and clinical outcome of osteosarcoma cases. Genotyping of six SNPs was performed in a 384-wellplate format on the Sequenom MassARRAY platform for 208 osteosarcoma patients to reveal any correlationsof the six SNPs with response to chemotherapy and clinical outcome. Individuals with the ABCB1 rs1128503 TTand ABCC3 rs4148416 TT genotypes had a higher probability of responding poorly to chemotherapy, indicatedby odds ratios (ORs) of 2.46 (95%CI, 1.21-5.74) and 3.78 (95% CI, 1.20-13.85), respectively. Moreover, theABCB1 rs1128503 TT and ABCC3 rs4148416 TT genotypes were significantly associated with shorter diseasefreesurvival (DFS) and overall survival (OS). Our study found the two SNPs in two transporter genes and onephase II metabolism enzyme to be associated with response to chemotherapy and overall survival in osteosarcomapatients, suggesting potential prognostic biomarker applications of the two SNPs.