ABSTRACT In Colombia serum and fecal samples from 307 asymptomatic lactating Holstein cows over three years of age from 14 herds with no previous diagnosis of paratuberculosis were taken. All serum samples were analyzed with a lipoarabinomannan based-ELISA (ELISA A). Positive and doubtful samples in ELISA A were analyzed with a protoplasmic antigens based-ELISA (ELISA B), including pre-absorption with Mycobacterium phlei. Fecal samples from animals positive in ELISA A were analyzed using a nested IS900-PCR and a F57 / ISMav2-real-time PCR. Fecal samples of animals from ELISA A-seropositive herds were decontaminated with 0.75% Hexadecylpyridinium Chloride and cultured on Herrold´s Yolk Agar medium. The same samples were decontaminated later with 4% NaOH and 5% oxalic acid and cultured on Lowestein-Jensen medium. Ten percent (31/315) of the samples and 70% (10/14) of the herds were positive with ELISA A. Only two animals of two different herds were positive with ELISA B. Six fecal samples were positive with PCR and only one was simultaneously positive in the two PCR types. Serological and PCR results did not always coincide. Cultivation was negative for paratuberculosis in all samples inoculated. However Mycobacterium engbaekii was isolated from LJ medium. Results confirm the presence of paratuberculosis in dairy herds in Colombia and demonstrate the limitations of available diagnostic tests for detection of subclinical infections, the determinant influence of ELISA type used, the low bacterial shedding in the cattle feces examined, the possible roll of other mycobacteria and the effect of conservation on the diagnosis of paratuberculosis