"A pregnant woman was infected by Zika and dengue and the foetus has shown various defects," the health authority of the Catalonia region said in a statement.
This was Spain's first case of Zika-related microcephaly, where babies are born with abnormally small heads and sometimes brain damage.
A total of 105 people in Spain have been infected with the mosquito-borne Zika virus, according to official statistics from May 3.
Spanish authorities have said all the infection cases -- including 13 pregnant women -- are "imported cases" found in people either "from, or who have visited affected countries" in Latin America.
Scientists believe the virus to be responsible for a surge in Brazilian infants born with microcephaly.
There is no vaccine or treatment for the virus, which in most people causes only mild symptoms -- a rash, joint pain or fever.
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