Often associated with China and India, sex-selective abortions have been growing in these regions since the early 1990s, according to the study from the National Institute for Demographic Studies (INED).
The study said the sex ratio in the South Caucasus countries of Armenia, Azerbaijan and Georgia and in parts of the Balkans, in particular Albania, had reached between 110 to 117 boys to 100 girls.
The ratio is considered officially out of balance when it hits 105 boys to 100 girls.
"In the three Caucasus countries, the ratio increased during the 1990s and reached levels higher than current estimates for all of India," the study said.
The imbalance is highest in Azerbaijan, where it has reached 117 boys to 100 girls, making it the least balanced country after China, the report said.
In the western Balkans, including Albania, Kosovo and Montenegro, the imbalance is less emphatic, at 110-111 boys for 100 girls.
But the report said "their regularity over the years attests to the reality of the imbalance."
"The persistance of traditional patriarchal values remains at the heart of the preference for male births in these regions," the institute said.
It said such attitudes had been reinforced in these regions amid the chaos and rampant poverty that followed the 1991 Soviet collapse.
"Family structures become the most important social institution," it said.
"The recent decline in fertility and the emergence of modern health services -- consecutive with the change in political and economic regimes -- have strengthened the desire for pre-natal sex selection," it said.
The study was unable to explain however why other countries in the Balkans or the post-Soviet nations of Central Asia had not seen similar increases.