Diagnosis of leptospirosis in Colombia is based on clinical history and serological testing. However, disease symptoms are nonspecific and there is no uniform criteria regarding the qualifications considered positive. Therefore, it is important to identify and characterize genes associated with pathogenicity in native strains for the development of new diagnostic tests and vaccine production. The aim of this study was to identify the ompL1 and lipL32 genes in Leptospira strains isolated from urine samples of cattle. Sixteen strains were obtained from urine samples and, DNA was isolated to perform two Polymerase Chain Reaction (PCR) tests which identified lipL32 and ompL1 genes. As positive control, a reference strain of L. interrogans was used. L. biflexa and Escherichia coli strains were used as a negative control. In 100% of the samples were identified amplicons of 960 bp and 423 bp corresponding to ompL1 and lipL32 genes respectively. Thus, the pathogenic property and conservation of genes in the isolated strains were confirmed. This study is presented as a contribution to the diagnosis of leptospirosis to use these genes as molecular markers of infection. The results of this study might provide clues for future clinical, epidemiological and molecular research leading to implement new diagnostic strategies and to expand knowledge of the pathophysiology of a disease of public health impact on human and animal.