Bladder cancer like other cancers arises from the accumulation of many genetic and epigenetic changes that lead to the activation of proto-oncogenes or inactivation of tumor suppressor genes. We aimed to investigate the methylation patterns of Twist homolog 1 (TWIST1) and nidogen-2 (NID2) genes in bladder cancer. Fifty six histologically confirmed bladder tumor samples and paired 24 urine samples constituted the study group and was compared with 15 age- and gender-matched noncancerous individuals. DNA was purified from both tumor and urine samples. The methylation status of the two genes was analyzed by methylation-specific polymerase chain reaction (MSP) in both urinary bladder cell carcinoma samples and urine samples. Sensitivity and specificity values of the method were assessed and compared with the results of the cytology test. Methylation of TWIST1 and NID2 was detected in 98.2% and 96.4% of the tumor samples, and in 87.5% and 95.8% of the urine samples, respectively. The sensitivity of TWIST1 and NID2 genes (87.5% and 95.8% in urine samples, respectively), was higher compared with urine cytology (62.5%) for cancer detection. The sensitivity of any of the two genes was 88.8% (8/9) for low-grade cases. The sensitivity of urine cytology was 33.3% for the same low-grade cases. To be used in the early noninvasive diagnosis of bladder cancer, the combined methylation analysis of TWIST1 and NID2 genes may be a simple, noninvasive, sensitive, and specific method for detecting cancer cells in urine.