Background Schizophrenia (SZ) is a neurodevelopmental disorder linked to evolutionary trade-offs for human-specific cognitive abilities, with sex-specific differences in clinical presentation. Cortical sulcal patterns, tightly linked to neurodevelopment and evolution, are shaped by the deepest and earliest-forming points of the cerebral cortex, named sulcal pits. In healthy individuals, sulcal pits patterns capture interindividual variability and are sensitive to sex-specific developmental differences (Hostalet et al., 2025); however, their spatial organization and sex-specific effects remain unexplored in SZ. Integrating sulcal pits patterns with genomic and transcriptomic data can reveal how genetic factors shape cortical architecture and SZ vulnerability. Human Accelerated Regions (HARs), conserved genomic regions with human-specific changes, may link evolutionary and developmental mechanisms, as their prenatal expression influences cortical morphology in SZ (Guardiola-Ripoll et al., 2023). Accordingly, we will present data on: i) divergence of sulcal pit patterns in SZ versus controls across lobes and hemispheres, highlighting sex-specific effects; and ii) the contribution of HARs-related gene expression to these differences. Methods The sample included 426 adults (237 SZ patients/189 healthy controls (HC)) with T1-w MRIs. Sulcal pits were extracted from FreeSurfer-derived white matter surfaces. Graphs were created for each lobe and hemisphere, considering sulcal pits as the nodes and their interconnections as the edges. Sulcal graphs were compared between patients with SZ and HC based on different sulcal pits features (position, depth, area and topology). Transcriptomic data (BrainSpan) included 179 HARs-related genes expressed in three specific prenatal stages: 13, 21, and 37 post-conception weeks. Covariation between transcriptomic data and the differences in sulcal pits patterns between patients and healthy individuals was tested by Partial Least Squares Regression (PLS-R) models. The analyses were performed separately in males and females. Results Males with SZ exhibited reduced sulcal pits similarity to HC in the left frontal lobe, while females showed reduced similarity in the right parietal lobe. PLS-R models identified that the expression of a gene tightly related to the emergence of human-specific abilities, FOXP2, was related to differences in the sulcal patterns between patients with SZ and HC across all prenatal stages, unveiling sulcal pits as neurodevelopmental and evolutionary markers of schizophrenia. Discussion Sulcal pits emerge as sex-specific early neurodevelopmental markers in SZ. These findings provide the first evidence of HARs-driven transcriptional influence on sulcal pits patterns, supporting the neurodevelopmental and evolutionary component of the disorder.