The cash, almost £500,000 more than last year's contribution, will support the overall continual running costs of the Wellcome Collection.
"This generous gift aid of profits is a tremendous support. The Conference Centre team has achieved great success over the past year despite the turbulent economic climate," said Wellcome trust director of medicine, society and history Clare Matterson.
The Conference Centre opened in May 2007 and comprises a 150-seat auditorium, four meeting rooms and open break-out spaces.
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