Abstract Background Cystic fibrosis (CF) is caused by mutations in the gene encoding the CF Transmembrane Conductance Regulator (CFTR) protein, resulting in compromised pulmonary function, malabsorption, and pancreatic insufficiency. The sequelae of CF are heterogeneous, and contributing factors are multifactorial. Nutritional deficiencies, particularly in essential fatty acids (EFA) and vitamins, are known to alter the trajectory of CF unfavorably. The current treatment modalities focus on proactive management of the pulmonary, gastrointestinal, and pancreatic functions; however, information on the monitoring and treatment of nutritional deficiencies in CF patients is scant. The objective of our study was to evaluate the effects of pancreatic function and CFTR modulator therapy on pertinent nutritional deficiencies in children and adolescents diagnosed with CF. Methods The study was approved by our institutional IRB and included 77 non-fasted CF participants, 10.4 + 5.2 years of age (range: 4 months-18 years), and an equal ratio of both sexes. Participants were stratified as pancreatic sufficient (PS, n=6), and pancreatic insufficient with (PI, n=48) or without CFTR modulator treatment (PI-M, n=23). Twenty-two fatty acids were measured in plasma by GC-MS, including omega-6 linoleic acid (LA), and omega-3 α-linoleic acid (ALA). Medical records and 24-hour dietary recalls were reviewed to correlate biochemical and clinical findings. Vitamins A and E and zinc levels of the participants were also obtained. Data analyses were performed by one-way ANOVA and Tukey’s multiple comparisons using Prism software (LaJolla, CA). Results There were no significant differences in BMI and caloric intake among the groups. The concentrations of EFA, LA, and ALA were significantly higher in the PS group (3904±229 nmol/mL and 149±24 nmol/mL) compared to the PI (2387±89 nmol/mL and 53±4 nmol/mL, p<0.01) and PI-M (2335±159 nmol/mL and 58±7 nmol/mL, p<0.01) groups, respectively. Similarly, the biologically active omega-6 arachidonic acid and omega-3 docosahexaenoic acid were lower in the PI and PI-M groups compared to the PS group (p<0.05). Interestingly, EFA deficiency biomarkers, omega-9 mead acid, and the Triene:Tetraene ratio, were significantly higher in the PI group (17±2 nmol/mL and 0.033±0.003) vs PS group (13±3 nmol/mL and 0.019±0.002, p<0.05), respectively. Higher concentrations of vitamins A and E were observed in the PS group vs PI-M groups (p<0.05), and zinc concentrations were not different among the groups. There were no associations between the concentrations of EFA and BMI, age, total caloric intake, and % calories from fat in PS, PI, and PI-M patients. Conclusion While advances in CF therapeutics are remarkable, our data show the persistence of nutritional deficiencies in pancreatic insufficient CF patients regardless of CFTR modulator therapy and support the clinical utility of EFA and vitamins as potential adjuvant biomarkers to assess the severity and assist in the clinical monitoring of CF.