Milk is one of the most important foodstuffs and raw materials in the food industry. As the first complete food available to infant mammals, it is bioactive and it contains all the indispensable nutrients. Organic farming is deemed to produce high quality food under sustainable conditions and, at the same time, to protect the natural environment within the farm. However, the most recent food and nutrition research does not confirm the extensive health benefits related to the consumption of organic products. The objective of the research study was to evaluate and compare the quality of commercial organic and conventional cow’s milk as regards the contents of some selected mineral compounds. The research was conducted on the organic and conventional cow’s milk available on the market in Southern Poland. The milk samples were analysed for the concentration of selected minerals contained therein, including some selected toxic metals; the analyses were performed with the use of flame atomic absorption spectrometry, atomic emission spectrometry, and graphite furnace atomic absorption spectrometry. The results of the research show that, in terms of the contents of micro- and macroelements, the organic and conventional milk do not differ significantly. The differences were found only between the amounts of sodium and manganese. The organic milk contained, on average, a statistically significantly smaller amount of those elements. Moreover, the presence of lead was detected in one type of the organic milk, although its amount determined (5.24 mg/l) was within the acceptable limits. Cadmium (amounting to 0.12 and 0.15 μg/l) was found in the two types of milk derived from the same company and in one type of organic milk; however, its concentration in the latter milk type was at a relatively low level (0.04 μg/l).