Massachusetts State Route 99 runs north-south in Suffolk County. It runs from U.S. Rt. 1, to the Essex/Middlesex County Line. MA St Rt 99 passes through the following town in Suffolk County. Charlestown MA St Rt 99 is not multi-plexed in Suffolk County. MA St Rt 99 intersects the following highways in Suffolk County. U.S. Rt. 1, at Charlestown. Massachusetts State Route 38, at Charlestown.