Cystic fibrosis patients are characterised by disorders of fat-soluble vitamin absorption and bone metabolism. The aim of this study was to compare the effect of 3-month supplementation with calcitriol and cholecalciferol on calcium–phosphate balance in patients with cystic fibrosis. The study included 23 cystic fibrosis patients aged from 6 to 19 years. It was a crossover, placebo-controlled trial. There were 3 visits during which blood and urine were collected for analysis. The patients were treated with cholecalciferol (1,000 IU/day) or calcitriol (0.5 μg 1,25OHD) and placebo, and then received medications according to the cross-over regimen. The second visit took place after 3 months. The concentration of calcium, phosphate, parathyroid hormone and 25OHD were determined in blood serum; calcium/creatinine index was determined in urine. It was shown that after 3-month supplementation with calcitriol, the phosphate concentration decreased significantly, from 1.48 mmol/L (±SD 0.27 mmol/L) to 1.35 mmol/L (±SD 0.20 mmol/L) (p = 0.021). The calcium concentration increased significantly after 3 months of calcitriol treatment, from 3.50 mg/dL (±SD 2.60 mg/dL) to 4.35 mg/dL (±SD 3.35 mg/dL) (p = 0.001). The level of parathyroid hormone decreased significantly after 3 months of treatment with calcitriol, from 36.54 pg/mL (±SD 17.61 pg/mL) to 29.36 pg/mL (±SD 13.08 pg/mL) (p = 0.019). In the cholecalciferol supplementation group, there were no changes in phosphate, calcium or parathyroid hormone concentrations. Supplementation with either cholecalciferol or calcitriol did not affect serum 25OHD levels. In patients with cystic fibrosis, calcitriol supplementation at a dose of 0.5 μg is safe and has a more beneficial effect on the calcium–phosphate metabolism and bone metabolism than that of cholecalciferol at a daily dose of 1,000 IU.