While 30 children died in the sick newly born care unit of the hospital alone, 19 others died at the time of delivery or soon after delivery at the hospital, a senior official said.
"A magisterial probe has now been ordered into the deaths. Hospital authorities have been booked for negligence," he said.
Deaths of children are becoming increasingly common at government hospitals in Uttar Pradesh.
Last week, as many as 42 children died at Baba Raghav Das Medical College in 48 hours in the state's Gorakhpur district.
More than 70 infant deaths were reported from the same hospital earlier last month, from various causes, including oxygen shortage.
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