Fermentation is a very crucial phase during the bread production process. A special type of microflora contained in the bread dough, mainly the yeast of a Saccharomyces type and/or lactic acid bacteria cause the dough to raise and a special bread taste and aroma to be produced; also, non-desirable microorganisms derived from flour to be blocked. During the fermentation process, a number of changes occur, the character of which has not yet been fully studied and which can affect food safety of the final product. To clarify the effect of fermentation process on the content of selected contaminants in major bread doughs, the content of the following elements was determined: cadmium, lead, mercury, chloro-organic pesticides residues, and ochratoxin A. Analyses were performed in the doughs immediately after the kneading and in the same dough bites after the fermentation and final rise were completed, i.e. just before baking. After the dough fermentation process, the content of toxic metals, especially of cadmium and lead, was found to be higher, and the content of chloro-organic pesticide residues was found to be lower. A substantial reduction in OTA content was a positive effect of the fermentation process.