Children with primary immunodeficiency diseases (PIDs), especially those with severe forms, have a high risk of malnutrition due to recurrent and severe infections. Patients with adequate nutritional status have better chances for more favourable outcome of PIDs. Therefore, it is important that the malnourished individuals are recognized and provided with nutritional support as soon as possible. The purpose of this study was to assess the nutritional status of children with PIDs. We aimed to determine if the nutritional status improved over time. We studied the nutritional status of patients who received hematopoietic stem cell transplantation (HSCT) as well. Furthermore, we were interested whether their nutritional status after the HSCT was comparable to a healthy population. The data on patient nutrition were obtained from 3-day dietary records and analyzed with the Prodi 6.7 Expert Plus software. All patients with PIDs under the age of 19, admitted to the Center for PIDs at the Pediatric Clinic in Ljubljana were invited to take part in our study. Thirty-eight patients participated in the assessment of nutritional status and fourteen of them filled-out their dietary records. Information about patients weight, height, body mass index (BMI) and type of treatment was collected retrospectively from the outpatient medical records. The nutritional status was evaluated using growth charts (weight, height and BMI for age). Our research showed that at the first examination, 13 - 18 % patients were malnourished, at examination after 1,5 - 3,5 years 3 - 24 % and at the last examination 3 - 13 %, depending on the criteria that we have used (weight, height, BMI for age). Patients who received HSCT were not malnourished at the last examination. We concluded that the diet of children with PIDs is inadequate. It was characterized by low energy intake and deficient intake of n-3 fatty acids, calcium, iron, copper, zinc and some vitamins (A, C, E, B12 and folic acid). In three patients (25%) we observed excessive protein consumption. The study confirmed that the proportion of malnourished children among patients with PIDs is relatively high and that their nutrition is inadequate. Incorporating the dietitian into the treatment of patients with PIDs is therefore essential.