It's believed they had syphilis. But no other major diseases come to mind- perhaps because of the comparative lack of domesticated animals, or the smaller and less connected geographic area (compared to Afro-Eurasia), and perhaps because severe disease mutations would likely burn themselves out within such regions rather than travel the length of Afro-Eurasia like old world diseases...
It's believed they had syphilis. But no other major diseases come to mind- perhaps because of the comparative lack of domesticated animals, or the smaller and less connected geographic area (compared to Afro-Eurasia), and perhaps because severe disease mutations would likely burn themselves out within such regions rather than travel the length of Afro-Eurasia like old world diseases...