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Differences between males and females in the fine-grained tissue structure of deep brain regions are minimal at ages 9 to 12 but emerge and widen during adolescence, according to a new brain imaging study. The timing coincides with puberty and with the period when sex differences in conditions like anxiety and depression begin to appear, though the study could not determine what drives the brain changes. The findings were published in Developmental Cognitive Neuroscience.
Deep gray matter refers to a collection of structures located beneath the outer layer of the brain. These areas include the amygdala, which processes emotions, the hippocampus, which is central to memory, and the nucleus accumbens, which plays a role in reward and motivation. The study also examined the thalamus, a relay hub for sensory signals, and the caudate and putamen, which help control movement and habits. In human populations, many mental health conditions tied to these brain functions show different rates of diagnosis between men and women, but the biological reasons behind these differences remain poorly understood.
Animal research points to puberty as a key period for these changes: a 2008 study in rats found that sex hormones during puberty drive the addition of new cells to brain regions that differ between the sexes. In humans, a 2014 study that followed young people over time found that pubertal development was linked to the size of these deep brain regions in both boys and girls, independent of age.
While overall volume provides part of the picture, scientists have sought to understand the microscopic layout of brain tissue. Earlier work by the same research team, covered by PsyPost in 2024, found large differences between young adult men and women in measures of tissue microstructure, with men showing signs of more densely packed cells in regions like the hippocampus. The new research, led by Christopher G. Filippi of The Hospital for Sick Children and Richard Watts of the University of Canterbury, aimed to pinpoint when those microscopic differences first develop.
The research team examined brain scan data from 1,643 individuals aged 9 to 35. The participants were drawn from two large public databases: the Human Connectome Project Development dataset for children and teens, and the Young Adult dataset for older participants. In their analyses, the scientists statistically controlled for age and body mass index, and they accounted for family relationships among the many twins included in the adult sample.
To evaluate tissue microstructure, the researchers used an advanced magnetic resonance imaging technique called Restriction Spectrum Imaging. This method measures how water molecules diffuse through brain tissue. Water trapped inside a cell encounters barriers, producing a restricted diffusion signal that reflects cell packing. Water in the spaces between cells encounters fewer obstacles, producing a hindered diffusion signal that reflects the extracellular environment.
For the youngest participants, aged 9 to 12, the researchers observed no statistically significant differences between boys and girls in these diffusion measures. Across the deep gray matter structures, the tissue composition in childhood appeared similar between the sexes.
However, differences began to emerge between ages 13 and 16, first in the hippocampus, amygdala, and thalamus. Restricted diffusion rose with age in both sexes, but from puberty onward it was consistently higher in males, a pattern the researchers suggest may reflect more densely packed cells or larger cell bodies. By ages 17 to 21, sex accounted for roughly 13 to 33 percent of the variation in restricted diffusion across all six regions, and in adults it explained 32 to 37 percent in the hippocampus and amygdala.
Females, in turn, showed a larger hindered component, meaning a greater share of the water signal came from the spaces between cells. Because both measures are expressed as shares of the total signal, the two patterns largely mirror each other.
In regions such as the nucleus accumbens, caudate, and putamen, females showed a slowing in development in their late teens before accelerating again in their early 20s, while males followed a more steady progression. By the mid-20s, the size of the sex difference in the hippocampus and amygdala had leveled off, though the measures themselves were still changing in both sexes. In the thalamus, the divergence between the sexes continued to widen up to age 35.
“Sex differences in the brain have so far been primarily investigated at the macro-structural level (i.e., differences in overall brain size or differences in the size of specific regions),” said Yumnah Khan, a doctoral scientist at the Autism Research Centre at the University of Cambridge who was not involved in the research. “What is interesting about this work is it provides evidence for differences in brain microstructure (i.e., what is happening at a finer level within brain tissue), which gives us a more detailed picture of sex differences in the brain.”
Marco Balducci, a senior researcher at the University of Turku who was not involved in the study, said the findings build on earlier work. “Earlier studies had identified sex differences in subcortical brain structure and, more recently, in diffusion-derived microstructure in young adults,” Balducci told PsyPost. “This study extends that work by showing that the differences emerge during adolescence rather than simply being present in adulthood.”
The timing of these changes aligns with the pubertal transition, leading the study authors to speculate about biological drivers. Earlier animal work indicates that sex hormones can influence synapses and dendrites, the connection points and branching extensions of nerve cells. Because these adolescent brain shifts occur alongside the emergence of sex-biased mental health conditions, identifying typical developmental paths could help clarify underlying vulnerabilities.
Khan told PsyPost that considering human imaging alongside animal research helps connect biology to observation. “Animal studies can provide much stronger evidence about causality and specific mechanisms, while human studies are generally observational and correlational,” she said. “However, when both of these lines of research are considered and interpreted together, we get a better picture of the mechanisms underlying sex differences in brain development.”
Balducci noted that the broad descriptive findings appear well-supported. “The main descriptive finding appears robust because the study uses a large combined sample, finds a consistent developmental pattern across several brain regions, and applies correction for multiple comparisons,” he said. “However, the reasons for these differences remain uncertain because the data are cross-sectional, and in this setting it is difficult to distinguish age-related changes from pubertal development or establish a hormonal cause.”
As with all research, there are a few things to keep in mind. The study relied on cross-sectional data from different individuals at each age, rather than following the same individuals across their development. Additionally, puberty was measured using ratings of physical development, which rose so closely with age that the researchers could not separate the effects of puberty from those of getting older, and hormone levels were not measured. The researchers did find an association between a girl’s first menstrual period and a specific measure in the thalamus, but they describe any role of sex hormones as speculative.
The researchers also had to combine two projects that used different scanners and imaging settings. Because one covered ages 9 to 21 and the other ages 22 to 36, the statistical adjustments for those differences fall at the same point as the transition into adulthood, so features of the age trajectories near that point, such as the slowdown seen in females, should be read with some caution. Comparisons between males and females within each age group are less affected.
“I think the biggest risk is interpreting these findings as showing that male and female brains are fundamentally different,” Khan said. “In reality, sex differences in the brain tend to be relatively small, with a lot of overlap between the sexes.”
She added that the timing of differences depends on which ages a study covers. “It is also important not to assume that adolescence is when these differences necessarily begin,” Khan noted. “Although the study found minimal differences early in childhood, sex-by-age effects can be highly sensitive to the particular age range that is being studied. As such, the findings do not necessarily mean that differences are entirely absent earlier in development.”
Balducci also cautioned against reading too much into what the scans can show.
“The findings do not show that differences in water diffusion directly cause differences in behavior or mental health,” Balducci pointed out. “Diffusion MRI provides an indirect measure of tissue microstructure.”
“Also, as with many sex differences, males and females vary on average,” Balducci added. “However, when multiple small differences are considered together, the overall profiles of males and females can become considerably more distinct.”
To address these remaining questions, both outside researchers point toward the need for investigations that capture earlier and more detailed developmental data.
“The most important next step would be a longitudinal study that repeatedly scans the same individuals before, during, and after puberty, while also measuring pubertal hormones and developmental phases,” Balducci told PsyPost. “That would help determine whether the observed diffusion changes track individual pubertal development and whether they are related to later mental-health outcomes.”
“It would be very interesting to see this approach being used in earlier stages of development, such as the prenatal period,” Khan said. “The prenatal period is another critical window for the emergence of sex differences in the brain. Moreover, male and female fetuses are exposed to different levels of sex hormones, which may contribute to differences in early brain development.”
The researchers say the sex-specific trajectories they describe could serve as a reference point for future studies exploring how departures from typical development might relate to mental health conditions.
The study, “Sex Differences in Human Deep Grey Matter Microstructure Emerge During Adolescence,” was authored by Christopher G. Filippi, Jay N. Giedd, Aziz M. Uluğ, and Richard Watts.