They say an 80-year-old man and a 32-year-old woman are the first two "probable" human cases in the city so far this year.
The elderly man has been hospitalized while the woman is recovering at home.
The suspected cases come a day after the city said that more than half of its mosquito traps have tested positive for West Nile — a record since monitoring started a decade ago.
Meanwhile, York Region officials say their mosquito pools have the highest number of West Nile bugs since 2006.
The virus can include flu-like symptoms, but many cases go undetected.