Previous studies have shown that girls reach puberty younger, become sexually active earlier and are more likely to get pregnant in their teens if their fathers are absent when they were young.
Other work has suggested that sons of missing dads have lower self-esteem later in life.
The latest study looked for biological changes in laboratory mice when they were raised without fathers.
A team at McGill University Health Centre in Montreal, Canada, used a strain of mice, which, like people, are usually monogamous and tend to rear their young pups together.
They removed the fathers from some of the mouse pups three days after birth until they were weaned at 30 to 40 days old.
The scientists, led by Dr Gabriella Gobbi, then analysed the behaviour and brain cells of the pups - and compared them to mice brought up with both parents.
Brain cells in the 'single parent' mice had a muted response to the 'cuddle hormone' oxytocin, a feel-good chemical released in the brain during sex or moments of intimacy.
That meant they were less likely to feel positive when in the company of others. The fatherless mice were also more anti-social.
"Usually if you put two animals in the same cage they investigate and touch each other, but when we put to animals deprived of a father together they ignored each other," New Scientist quoted Gobbi as saying.
Her colleague Francis Bambico presented the work at the World Congress of Biological Psychiatry in Paris, France, in early July.
The scientists are unsure whether the same biological changes take place in human children raised without a father - and whether the findings are applicable to people.
In the strain of mice used in the experiment, the fathers lick and groom the young pups more than the mothers do. Because grooming affects the development of pups, it could be the lack of physical contact that cause the changes in the brain, the researchers say.
The finding follows another study, which showed that men experience a huge surge in oxytocin after a child is born.
Dr Ruth Feldman of Bar-Ilan University in Ramat-Gan, Israel tested oxytocin levels of 80 couples before a child was born and six months afterwards.
She found that levels of the feel-good chemical rose in mothers and fathers after the arrival of a child.
The chemical affected the parents in different ways.
Mothers with the highest levels spent much longer gazing at their children, stroking and kissing them and speaking in a "sing song" voice, she found.
Dads with the highest levels played more with their child than fathers with the lowest levels.
"Fathers and mothers contribute in a very specific and different way," said Feldman, who presented the results at a Society for Research in Child Development meeting in Denver, Colorado, in April.
She believes fathers may be 'biologically programmed' to help raise children.