Fluorine and aluminum are able to pass through the blood-brain barrier and accumulate in the central nervous system (CNS) of exposed animals. Chronic intoxication is accompanied by behavioral disorders, degenerative changes, and abnormalities of aerobic metabolism of the neurons. Awareness of the role of aluminum in Alzheimer’s disease stems from epidemiological studies demonstrating increased prevalence of this condition in areas with relatively high content of aluminum in drinking water. The uptake of aluminum in the gastrointestinal tract is decreased in the presence of iron, calcium, magnesium, phosphate, or fluoride. Many magnesium-containing enzymes are affected by aluminum, which is able to replace magnesium and thus reduce their activity. The purpose of this study was to determine the concentrations of fluorine, aluminum, and magnesium in some structures of the CNS of rats exposed to fluorine and aluminum in water. Our material consisted of 64 Wistar rats divided into eight equal groups. Groups I, II and III were female rats exposed, respectively, to 100 ppm fluorine ions, 300 ppm aluminum ions or both at same doses alternating every second day. Groups IA, IIA and IIIA consisted of male rats exposed like the respective female groups. Control groups K1–females and K2–males received distilled water ad libitum. Exposure lasted 31 days whereupon the animals were anesthetized with ketamine and sacrificed. The brain was collected and the cerebellum, brain cortex, and hippocampus were isolated. Concentrations of fluorine, aluminum, and magnesium were measured with prior mineralization of wet tissues in a microwave oven. Fluorine concentrations were determined with a potentiometric method and ion-selective electrode. Aluminum was measured with ICP (inductively coupled plasma) and magnesium with ASA (atomic absorption spectrometry). The highest concentrations of fluorine were observed in rats exposed to fluorine only. The same pattern was true for aluminum. Groups exposed alternatively to both elements demonstrated lower accumulation of fluorine whereas accumulation of aluminum did not change significantly. Apparently, aluminum reduced the availability of fluorine but there was no reciprocal effect. No significant changes in the concentrations of magnesium were noted, regardless of the brain structure or group. It can thus be concluded that exposure to fluorine, aluminum or both has little effect on the concentration of magnesium in the CNS of rats.