Bovine leptospirosis is a highly prevalent infection worldwide causing serious losses in cattle production and serving as a source for human infection. Diagnosis and assessment of prevalence of this infection in bovine herds is difficult due to limitations of current procedures. The present report describes the adaptation of a polymerase chain reaction (PCR) protocol for detection of leptospiral DNA in bovine urine. The amplification products corresponded to a segment of the Leptospira 16S rRNA gene detected using two sets of primers (A/B and C/D). A total of 547 urine samples from Bos taurus (n=327) and Bos indicus (n=220) were collected from animals in Andean and Coastal regions of Ecuador, either by furosemide-induced urination or from bladders at the slaughterhouse. The results of this research showed a PCR positivity of 13.52% using primers A/B. Bos taurus samples obtained by urination and those obtained from bladder showed a significant difference in PCR positivity (P= 0.036). Differentiation of Leptospira species was preformed by DNA sequencing of the amplified products. Three amplicons showed 90 and 98% sequence identity with L. borgpetersenii and 98% identity with L. inadai. The results of this study suggest that PCR could be an excellent approach for epidemiological studies.