Morphological abnormalities of subcortical structures have been consistently reported along the schizophrenia clinical spectrum, and they may play an important role in the pathophysiology of psychosis. However, the question arises whether these subcortical features are consequences of medication and illness chronicity, or if they contribute to the vulnerability to develop schizophrenia spectrum disorders. If some of the subcortical abnormalities could be evidenced in community adolescents expressing higher schizotypal traits (psychometric schizotypy), they could potentially shed light on vulnerability markers. To date, very few studies have examined the link between psychometric schizotypy and volumes of subcortical regions, and none of them have used a longitudinal design. This study sets out to investigate developmental trajectories of subcortical volumes in 110 community adolescents (12 to 20 years old), for whom MRI-scans were acquired over a period of 5 years, reaching a total of 297 scans. Analyses were conducted using Freesurfer, and schizotypal traits were measured with the Schizotypal Personality Questionnaire (SPQ). Using mixed model regression analyses following a region-of-interest approach, we observed differential linear developmental trajectories in four subcortical structures when comparing higher versus lower scorers on the disorganized schizotypy dimension (bilateral hippocampus, left-lateral ventricle and left-pallidum) and the negative schizotypy dimension (bilateral pallidum, and right-thalamus). All results survived a threshold of p < .05 (FDR-corrected) while covarying for the effect of other psychological problems (externalized and internalized psychopathology). These results indicate that expression of higher levels of negative and disorganized schizotypy during adolescence was associated with neural markers linking schizotypy personality features to schizophrenia spectrum disorders.