With the recognition of their ability to promote weight loss, conjugated dienes of linoleic acid (CLA) have become the main ingredient of certain dietary supplements to counteract obesity. The results of prospective studies, however, indicate there may be long-term side effects that could be of key importance for the safety of CLA-based products. The aim of this study was to examine the effect of CLA supplementation with the effective weight-reducing trans-10, cis-12 CLA, its ineffective companion cis-9, trans-11 CLA, and 1:1 mixtures of them on the mineral composition of hard tissues and blood in mice. The study material consisted of bones, teeth, and serum of female obesity-prone C57BI/6J mice fed MURIGRAN feed containing soy oil or soy oil plus CLA. After 4 weeks of supplementation, the animals were sacrificed and the tissues were collected for analysis. The fluoride content was determined by potentiometry, while calcium and magnesium levels were determined by atomic absorption spectroscopy. The results showed that CLA isomers significantly increased the bone fluoride content while reducing the fluoride levels in teeth and serum, which was particularly evident in case of the CLA cis-9, trans-11 isomer. With the latter, a slight reduction in the bone calcium content was also observed, accompanied by a statistically significant reduction of magnesium levels, which might have a significant impact on bone quality. It appears that calcium and magnesium are transported from bones to serum and teeth with CLA supplementation, wherein a rise in their levels was observed. In teeth, increased calcium and magnesium levels with simultaneous reduction in the fluoride levels occurred, thereby possibly reducing enamel hardness by increasing the formation of crystal defects and the presence of amorphous hydroxyapatite.