"We are counting fifty deformities within a period of two years," Eastern Cape spokesman Sizwe Kupelo said on Monday.

"We don't have a documented cause."

He said the most recent case was a baby girl born on Saturday at the Dr Malizo Mpehle district hospital in Tsolo, near Mthatha.

"She was born with a small penis on the forehead and one eye on the forehead," Kupelo said.

"She was born with no nose and where there are supposed to be eyes there was nothing, just skin covered over the area."

Kupelo said the baby, born to a 16-year-old, was taken to the Nelson Mandela Academic hospital, but died on Sunday.

Earlier this month, a pair of conjoined twins were born also at the Dr Malizo Mpehle district hospital in Tsolo.

Kupelo said at the time that they were the fifth set of conjoined twins born in the former Transkei in the past 18 months.

He said most of the babies being born with deformities were from the former Transkei.

Deformities, besides conjoined twins, included babies being born with their heart or brain exposed, having two penises or four legs.

Last year in November, a Port Elizabeth baby boy born with his heart outside his chest died after an emergency operation.

Kupelo said doctors in the area, were "in the dark" about the causes.

"This calls for a need for specialists to conduct a study in the area so as to determine what is the cause."

The department was "in talks" about the urgent need for research by paediatric specialists into the problem.

Kupelo said most of the babies with deformities died soon after birth, or during procedures to try and rectify the deformities.

"Where necessary we attempt procedures but unfortunately the majority die," he said.