Zika has swept through much of Latin America, prompting the World Health Organization (WHO) to declare an international public health emergency in February 2016.
The main hospital in Guatemala's capital has confirmed the country's first case of a Zika-linked birth defect in a newborn and two cases of a related nerve disorder.
A 70-year-old man and a five-year-old girl were diagnosed with Guillain-Barre syndrome, a neurological autoimmune condition which can cause paralysis, Carlos Mejia, head of the infectious diseases clinic in the Hospital Roosevelt, told a news conference.
Microcephaly is where babies are born with abnormally small skulls and underdeveloped brains.
Zika is most commonly transmitted by mosquito, although rarer cases of transmission through sex have been identified.
Mejia said tests were being carried out out on two other babies to determine whether their mothers had contracted Zika while pregnant.
He added that there have been no confirmed deaths from conditions linked to the virus, but there was a report of a man infected with Zika dying of severe pneumonia.