Background: Cerebral palsy is one of the most common causes of movement disorders in children, whilst myelomeningocele is the most severe form of spina bifida. Both motor dysfunctions result in chronic immobilisation that can lead to secondary low bone mass and even osteoporosis. In this context, risk factors for osteoporosis may also include low calcium and vitamin D intake from diet and long-term use of anticonvulsants or glucocorticosteroids. Long-bone and vertebral fractures in the course of secondary osteoporosis in children with significant motor activity limitation deteriorate their quality of life. The aim of the study was to assess the bone mineralisation status and vitamin D concentrations in children and adolescents with motor disabilities in the course of cerebral palsy and myelomeningocele. Materials and methods: We analysed data from medical records of 35 children aged 3–18 years, including 20 children with cerebral palsy and 15 children with lumbar myelomeningocele. Selected parameters of calcium and phosphate metabolism, including serum 25-hydroxyvitamin D levels, and the results of a bone densitometry, using dual-energy X-ray absorptiometry in two paediatric measurement programs were assessed. Z-score equal to or lower than −2.0 was considered as criterion of low bone mass diagnosis. In 22/35 children the indications for diagnostics was motor disability (mainly) as well as long-bone and/or vertebral fractures. Results: Low bone mass was diagnosed in 27/35 evaluated patients, while osteoporosis in 16/32 patients. Vitamin D concentration not exceeding 30 ng/mL was found in 21/35 (60%) children. Conclusions: Measurements of bone mineral density in children with motor disabilities should be included in multidisciplinary medical care. In this group of patients the vitamin D in doses depending on its serum concentration may be used either prophylactically – before bone fracture – or curatively – after being diagnosed with osteoporosis.