T-2 toxin and deoxynivalenol (DON) are two representative mycotoxins that are commonly found in cereals and agricultural products. As T-2 toxin and DON are considered the cause of Kashin-Beck disease, a special osteoarticular disease, chondrocytes would be a vital target site for these toxins. To fully understand the toxicity effects of T-2 toxin and DON on chondrocytes, the present study investigated and compared the gene expression profiles and underlying mechanisms of T-2 toxin and DON on cultured human chondrocytes by microarray and bioinformatics analysis. Normal human chondrocytes were treated with T-2 toxin at 0.01 μg/ml and DON at 1.0 μg/ml for 72 h and analyzed by microarray using Affymetrix Human Gene Chip. Comprehensive analysis, including gene ontology, pathways and gene-gene networks was performed to identify the crucial gene functions, related signal pathways and key genes. A total of 175 and 237 differentially expressed genes were identified in human chondrocytes for T-2 toxin and DON treatment, respectively. Of these, 47 had the same expression tendencies in the two groups. The protein-protein interaction network analysis showed that the 10 hub genes were different between the two groups. Our results provide a comprehensive understanding of the toxic mechanism of T-2 toxin and DON on human chondrocytes and suggest that although T-2 toxin and DON showed some similar toxic mechanisms in human chondrocytes, they also had different toxic characteristics.