The purpose of this work is the evaluation of the nutritional status of patients with cystic fibrosis (CF), based on the level of vitamin C in urine and vitamins A and E in serum, using the fast, selective and fully automated micellar electrokinetic capillary chromatographic (MEKC) and microemulsion electrokinetic capillary chromatographic (MEEKC) methods. The optimization of parameters affecting the electrophoretic separation provided adequate separation of the analytes of interest in the short time of 8 min (MEKC) and 20 min (MEEKC). The developed methods were practical applications to evaluate the levels of vitamins A, C and E in real samples from 28 children suffering from cystic fibrosis and from 10 healthy volunteers. Based on the mean concentration values obtained in the two groups, it can be seen that the levels of each vitamin were lower in patients with CF than in healthy volunteers. In the case of vitamin E, these differences in both groups were statistically significant, while the disproportion of concentrations of vitamins A and C in both the studied groups were not so relevant. On the other hand, a principal component analysis (PCA) confirmed that in some patients with CF the concentration of vitamin A was significantly lower than in the control group. Thus, the future evaluation of the status of fat-soluble vitamins in the longer term for the evaluation of the nutritional status of patients with CF should be continued. The presented CE methods can become useful tools for the evaluation of the nutritional status of patients with CF.