The objective of this study was to determine the concentrations of Cu, Cd, Pb, Mn, Cr, Co, Ni, Zn, and Hg in the white and fruit parts of commercially available yogurts (n = 30) from Nitra markets (Slovak Republic). The results were correlated to determine their relationships. Three yogurt fruit flavors were chosen and tested, strawberry (n = 10), blueberry (n = 10), and cherry (n = 10). The elements were analyzed using atomic absorption spectrophotometry. Higher concentrations of toxic elements, such as Cd and Pb, were found in the fruit parts of the yogurt, and in some cases, the tolerable limit was exceeded. The white part of the yogurt was not contaminated by toxic elements. White yogurt is a good source of nutrients for humans, but the fruit part in yogurt requires detailed monitoring and improvements in the processing techniques.