Background: Cystic fibrosis (CF) is a multisystem disease presenting different manifestations, including the involvement of the respiratory and gastrointestinal tract. Patients may be at risk for micronutrient depletion, particularly during illness and infection. However, the relationship between micronutrient depletion and pulmonary involvement is not established well. Objectives: This study aimed to determine the relationship between serum levels of calcium, phosphorus, magnesium, zinc, copper, selenium, and vitamin D with the severity of pulmonary involvement in patients with CF. Methods: This cross-sectional study was performed on 84 patients with CF referred to Mofid Children’s Hospital, Tehran, Iran, in 2017. The collected data included demographic and anthropometric information. Laboratory evaluations included magnesium, copper, zinc, selenium, complete blood cell count (CBC), and vitamin D levels. The severity of pulmonary involvement was determined based on the Brasfield scoring system (BSS). Pearson correlation coefficient, t test, χ2 test, or Fisher exact test was used for analyses. Results: The mean age of the children was 6.8 ± 3.5 years, and 36 patients (43%) were female. Based on the z score, 53 patients (63%) were malnourished. The severity of pulmonary involvement was mild in 25 patients (30%), moderate in 39 patients (46%), and severe in 20 patients (24%). The percentages of deficiency related to vitamin D, zinc, copper, and selenium were 56%, 38%, 32.1%, and 21.4%, respectively. Among trace elements, there was a statistically significant relationship between the severity of pulmonary involvement according to BSS and serum copper (P = 0.007 and r = -0.229) and selenium deficiency (P < 0.001 and r = -0.418). There was a significant relationship between malnutrition and vitamin D deficiency in patients (P = 0.034, r = 0.231). Conclusions: Serum copper concentration might affect respiratory function in CF patients. Selenium supplements should be added to patients’ diets. However, further interventional studies are required to investigate the possible causal relationships.