To identify adenovirus in patients with conjunctivitis by molecular methods such as the Polymerase Chain Reaction (PCR) and DNA sequencing. Samples of scrapings from the inferior fornix of 51 patients (39 diagnosed with Follicular Conjunctivitis and 12 diagnosed with Vernal Conjunctivitis) were processed by generic PCR to identify adenovirus. All the samples that were PCR positive were cultured on VERO cells for virus isolation, with this being demonstrated by immunofluorescence. For the identification of the isolated serotype, the multiplex PCR was utilized and DNA automated sequencing was employed to identify the genetic variants. Twenty-eight of the individuals diagnosed with Follicular Conjunctivitis and six of those diagnosed with Vernal Conjunctivitis, had positive results to adenovirus (67%). The cultures in VERO cells allowed the isolation of eight samples. Only three of the isolated viruses (one Ad1 and two Ad2) were identified by the multiplex PCR used to identify the subgenus C adenovirus. An Ad1 genetic variant was identified by automated sequencing while the Ad2 serotypes were identical to the ones reported by Genbank. The Polymerase Chain Reaction and DNA sequencing are useful tools to identify and characterize microorganisms responsible for diseases such as conjunctivitis caused by adenoviruses.