Consumption of ochratoxin A (OTA) contaminated diets results in economic losses to the poultry industry. The objective of the current study was to evaluate the effects of quantity and time of exposure to dietary OTA on performance, organ weights, serum biochemistry, and gene expression in the kidneys of chicks. One hundred eighty day-old male broiler chicks (Ross 308) were randomly assigned to a 3 × 3 factorial arrangement of treatments (3 levels of OTA: 0, 1 and 2 mg OTA/kg diet and 3 time periods: 7, 14 and 21 d) with 4 replicate pens of 5 birds each per treatment. Birds fed 2 mg OTA/kg diet had decreased feed intake, body weight gain and increased serum uric acid levels at 14 and 21 d, and also poorer feed conversion and increased relative kidney weight. Birds fed 1 mg OTA/kg diet had decreased serum total protein. At 21 d, birds fed 1 mg OTA/kg diet had decreased albumin, and aspartate aminotransferase concentrations. For RNA-Sequencing analysis (RNA-Seq), kidney samples were collected weekly from 3 controls and 3 chicks fed 1 mg OTA/kg. NextGENe software was used for read alignment and transcript quantification. Reads per kilobase of target per million tiled reads (RPKM) were used in the Student’s t test (P < 0.05, fold change >2). A total of 27,638,976 50-bp RNA-Seq reads were produced over the 3 time periods. Transcripts (40,782) were assembled de novo and annotated by homology to either G. gallus or H. sapiens. Genes associated with carbohydrate and amino acid metabolism were downregulated and genes associated with the immune system were upregulated at 7 and 14 d. Genes associated with lipid metabolism and xenobiotics biodegradation and metabolism were also downregulated at 14 d. These metabolic changes disappeared at 21 d, suggesting that damage to the kidney and other related organs was repaired or the damage was contained. In conclusion, the decreased performance and increased kidney weight and serum uric acid levels in birds fed 2 mg OTA/kg confirmed the nephrotoxic effects of OTA. The supplementation of 1 mg OTA/kg diet caused time-dependent alterations in renal gene expression in chicks.