Magnetic resonance imaging is an essential tool for the identification of neurological problems since it provides relevant information on brain development. The aim of the present work was the detection of neurological alterations in newborns from 4 to 12 months of age by segmentation and analysis of lateral ventricles in magnetic resonance images. For this purpose, an automated deep approach based on U‐net is proposed to segment the cerebral ventricles of the newborn. Subsequently, for these regions, features were extracted based on the patient's clinical history and on the shape (area, roundness, normalized central moment, among others) and pixel intensity (mean gray value, contrast level, among others). Once the features were extracted, different types of intelligent models (Logistic Regression, k‐Nearest Neighbors (kNN), and a Convolutional Neural Network) were assessed to detect the presence of neurological alterations. The segmentation phase of the system was tested on 50 patients and the classification phase on 28 patients (11 healthy, 17 with neurological changes). The results show a DICE similarity coefficient of 0.89 and a volume ratio of 1.05 for the segmentation stage and an accuracy of 98%, precision of 100%, sensitivity of 92%, and specificity of 100% for the classification stage using kNN. The last one proved to be the most computationally feasible model, due to the time required for training and inference (0.36 s and 35.2e‐4 s, respectively), as well as the consumption of computational resources (0.1 GB RAM CPU). In conclusion, it is possible to detect neurological alterations in newborns aged 4 to 12 months by segmenting and classifying the lateral ventricles in magnetic resonance images, using image processing techniques, the U‐net, as well as the kNN algorithm. This proposed methodology could play an important role in the early diagnosis and treatment of neurological disorders.