Christopher Evans, 41, was arrested Wednesday after good Samaritans spotted his children in an unlocked SUV.
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Police say the 4-year-old girl and 1-year-old boy had been alone for 20-minutes while their father was at a doctor's appointment.
It was 35 degrees out at the time.
Evans was charged with two counts of endangering the welfare of a child.
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He was held overnight and will be arraigned at First District Court in Central Islip on December 6.
The children were released to a family member.
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