Currently, the only treatment for coeliac disease (CD) is a strict, lifelong gluten-free diet (GFD); however, their completeness with regard to energy and macro- and micronutrients remains poorly understood. Paediatric studies are often limited by a low quality and a lack of controls, and their findings should be interpreted with caution. The aim of the present study was to evaluate nutritional imbalances in children with CD on a strict GFD. Methods: A single-centre prospective cohort study was conducted. A total of 48 children with CD (33 girls, mean age 11.8 ± 3.68 years) on a strict GFD (mean duration 5.02 ± 3.87 years) were compared with 50 non-coeliac subjects (26 girls, mean age 10.2 ± 3.97 years). In both groups, anthropometric measurements (body height, weight and BMI) and laboratory tests (haemoglobin level, calcium and magnesium serum concentration, folic acid, vitamin B1, B2, B6 and B12 level) were checked. Additionally, in coeliac subjects, a 3-day food record for energy and macro- and micronutrient intake assessment were determined, and the values were compared to those in non-CD participants and the dietary reference intake (DRI) standards. Results: The CD children were more likely to demonstrate significantly lower serum vitamin B1 and folic acid levels compared to controls (p = 0.01 and p = 0.002, respectively). Although mean serum calcium values were within normal ranges, they were significantly lower in CD subjects than controls (p = 0.01). Mean calcium, folic acid and vitamin D intake was below the dietary recommendations in the CD group (69.9%, 71.2% and 68.9% DRI, respectively) but did not differ significantly between CD and non-coeliac subjects. In turn, the mean supply of proteins and carbohydrates in the CD group substantially exceeded the recommended levels (190.3% and 189.4% DRI, respectively) but was similar to controls. A significantly higher number of CD children were classified as underweight, and a significantly lower number as overweight or obese, compared with controls (p < 0.001). Conclusion: Although children with CD receive nutritional education at diagnosis, a GFD often does not provide a balanced set of macro- and micronutrients. This is mainly due to unhealthy dietary habits, as commonly observed in the general population. Children with CD should be informed that while their diet should be free of gluten, it should nevertheless cover all their nutrition requirements in the long term.