Background: In recent years, rapid advances in diagnosis and treatment have been observed in spinal muscular atrophy (SMA) patients. The introduction of modern therapies and screening tests has significantly changed the clinical picture of the disease. The previous classification has, therefore, been replaced by new phenotypes: non-sitters, sitters, and walkers, defined by the patient's functional level. However, despite the change in the clinical picture of the disease, patients still suffer from accompanying structural disorders such as scoliosis or joint contractures. Their presence also significantly affects the acquisition of subsequent motor skills. Due to this, monitoring structural changes and ensuring therapists are aware of improvements or declines in patient functionality are essential components of clinical practice. This study aims to compare the assessment of structural and functional changes after a 12-month follow-up in SMA patients who have already experienced the effects of the disease and are now receiving modern therapy. Methods: We present a study of 34 SMA patients being treated with modern therapies and tested twice 12 months apart. The participants were tested using structural measurements and validated scales such as The Children's Hospital of Philadelphia Infant Test of Neuromuscular Disorders (CHOP-INTEND) and Hammersmith Functional Motor Scale-Expanded (HFMSE). Results: During the 12-month follow-up, patients showed deteriorating, non-statistically significant structural changes. We also proved that patients showed a trend toward functional improvement. Analyzing the individual scale items, we distinguished which participants obtained the maximum score for a given parameter and no longer had an opportunity to improve during the second examination. Conclusions: Our study proved that most patients improved overall motor function. The examination of structural measurements should become a standard in the evaluation of SMA patients.