The biggest concern people have with granite is that it can contain trace amounts of radioactive elements and produce radon over the life of the countertops. However, the EPA (Environmental Protection Agency) has deemed it safe for indoor usage. In fact, in some studies, no samples contained any significant amounts of harmful elements.
In general, soil will emit radon over time in a much more alarming amount than countertops. This is part of why people test for radon in their basements and may install a ventilation system to prevent any harmful accumulation of radon in their homes