J Oral Pathol Med (2012) 41: 568–576 Background:  Oral microbial flora and a damaged oral mucosa may increase the risk of bacteriemia, fungemia and complications in immunocompromised patients. Aim of the Study:  Assessment of presence: bacteria and Candida spp. in different oral lesions, and the incidence of bacteremia in the case of a damaged mucosa in transplant recipients and patients receiving anti‐tumour chemotherapy. Material and Method:  Forty‐five patients – 18 months to 18 years of life, were included (20 – organ recipients, 14– anti‐tumour chemotherapy, 11 – control group). Clinical, oral mucosa examination focused on the type, severity and site of lesions, and microbiology assessed the presence of bacteria and fungi in the material from lesions. Blood cultures were performed in ten immunocompromised patients with manifestations of systemic infection. The control material consisted of blood cultures made prior to the onset of oral lesions and after 4–6 weeks following their remission in a diagnosed bacteremia. The statistical analysis was performed. Results:  In the subjects with secondary immunodeficiency, among other coagulase‐negative Staphylococcus (CoNS), Candidia spp. were more frequent. In cancer patients, mucositis was associated with Candida spp., Streptococcus spp. Organ recipients with stomatitis exhibited the presence of CoNS, Streptococcus viridians and other. Oral lesions in the control group contained Haemophilus parainfluenzae, Neisseria spp. and Staphylococcus aureus. In 30% of immunocompromised patients, oral lesions were accompanied by bacteremia. Conclusions:  A correlation has been found between oral lesions and the presence of S. aureus in patients without secondary immunodeficiency, and of CoNS, Enterococcus spp., Candida spp. in immunocompromised patients.