The attenuated bacilli Calmette-Guerin (BCG) vaccine is administered worldwide to prevent tuberculosis and is considered to have an excellent safety profile. In Poland, since 1955 BCG mass vaccinations have been compulsory. More than 95% newborns and 80% of older children of the population have been vaccinated. Complications of vaccination are uncommon. Although BCG has been used safely for many years, it can cause disease in humans, especially those with cellular immunodeficiencies. The risks associated with BCG vaccination include local complications, extraregional localized disease, and disseminated BCG disease. Identification of M. bovis BCG in laboratory is a very difficult process. Routine identification of mycobacterial isolates in clinical laboratories involves culture of Mycobacterium tuberculosis complex which includes M. tuberculosis, M. bovis, M. africanum and M. microti and the vaccine strain M.bovis BCG. Most laboratories cannot quickly differentiate between BCG and other members of M. tuberculosis complex and some cases of BCG complications in children may be considered and treated as tuberculosis. Because of difficulties in proper identification of BCG strains isolated from the patients, the prevalence of BCG infections is not know exactly. Knowledge of BCG infection would be of particular interest to the clinician responsible for the therapy. We describe the several methods using in mycobacterial laboratory for identification and suggest the modern algorithm of BCG strains identification including mycolic acids profile by HPLC and 14C PZA resistance methods. The methods allowed us fast and accurate identify M. bovis BCG infection in 5 children which have been described in our paper. Preliminary diagnosis for four children among five tested was tuberculosis. One immunocompromised HIV negative child died, one still excretes BCG bacilli. To our knowledge, this is the first report of BCG complication (AEFI) in Polish children in which HPLC and 14 C PZA methods have been used for rapid identification of M. bovis BCG infection and/or complication.