Structural brain alterations found in Autism Spectrum Disorder (ASD) have previously been very heterogeneous, with overall limited effect sizes for every region implicated. In this study, we aimed at exploring the existence of subgroups in ASD, based on neuroanatomic profiles; we hypothesized that effect sizes of case/control difference would be increased in defined subgroups. Using the dataset from the ENIGMA-ASD Working Group (n=2661), exploratory factor analysis (EFA) was applied on seven subcortical volumes of individuals with ASD and controls to uncover the underlying organization of subcortical structures. Based on earlier findings in ADHD patients and controls as well as data availability, we focused on three age groups: boys (aged 4-14 years), male adolescents (aged 14-22 years), and adult men (aged >=22 years). The resulting factor scores were used in a community detection (CD) analysis, to cluster participants into subgroups. Three factors were found in each sample, with the factor structure in adult men differing from that in boys and male adolescents. From the patterns in these factors, CD uncovered four distinct communities in boys and three communities in adolescents and adult men, irrespective of ASD diagnostic status. The effect sizes of case/control comparisons appeared more pronounced than in the whole sample in some communities. Based on subcortical volumes, we succeeded in stratifying our participants into more homogeneous subgroups with similar brain structural patterns. The stratification enhanced our ability to observe case/control differences of subcortical brain volumes in ASD, and may help explain some of the heterogeneity of previous findings in ASD. ### Competing Interest Statement Dr. Arango has been a consultant to or has received honoraria or grants from Acadia, Angelini, Gedeon Richter, Janssen Cilag, Lundbeck, Minerva, Otsuka, Roche, Sage, Servier, Shire, Schering Plough, Sumitomo Dainippon Pharma, Sunovion and Takeda.Dr. Anagnostou has served as a consultant or advisory board member for Roche and Takeda. Dr. Freitag has served as a consultant for Desitin regarding issues on ASD.Dr. De Martino is a coauthor of the Italian version of the Social Responsiveness Scale, for which she may receive royalties. Dr.Rubia has received funding from Takeda pharmaceuticals for another projects. Dr. Buitelaar has served as a consultant, advisory board member, or speaker for Eli Lilly, Janssen-Cilag, Lundbeck, Medice, Novartis, Servier, Shire, and Roche, and he has received research support from Roche and Vifor. Dr. Gallagher received funding from the Meath Foundation and the National Children's Research Centre in Ireland. Dr. Parellada has served as a consultant, advisory board member or received honoraria from Sevier and Exeltis. She has received travel support from Janssen Cilag and Lundbeck. Dr. Murphy has served on advisory boards for Roche and Servier. Dr. Franke has received educational speaking fees from Medice. The other authors report no financial relationships with commercial interests.

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