An inquiry began after the mother's indifferent attitude to the birth of her baby girl on New Year's Day aroused suspicion among medical staff.
Social services found her brothers, aged two, five and six, living in the flat in a suburb of northern Paris.
It seems the boys had never left the flat in all their lives.
The two eldest had developmental problems, could not speak properly and had difficulty walking, as well as being undernourished.
They had simple mattresses for beds and there was no furniture, let alone toys, a judicial source told French daily Liberation.
All four children were taken into care in February.
The father, 33, and the mother, aged 27, are in custody being investigated on suspicion of depriving their children of care - a charge which could see them jailed for seven years and fined 100,000 euros (Â£83,500; $138,000).
News of the children being found has emerged in the French media only this week.
It appears that none of the boys attended school or received vaccinations or any other medical attention.
Neither parent worked but they received child benefit, Liberation reports.
It seems the family had been living in the seventh-floor flat in the deprived district of La Courneuve in the Seine-Saint-Denis suburb of Paris for six years.
Neighbours in the block of flats said they had never seen the elder boys.
Foster parents are now taking care of the two youngest children while the eldest are receiving specialist care.
One question being asked is why no follow-up was given to the boys, who had been born in France, the BBC's Hugh Schofield reports from Paris.
"Sometimes I saw the father as I was leaving for work but I never saw the children," an unnamed neighbour told Liberation.
"I would hear some noise, sometimes children crying, but that was all."
French authorities are investigating an Indian couple for neglect after their three small children were found living in appalling conditions in their flat.