Cusco and Machu Picchu are usually mentioned in the same breath, but the altitudes are different enough to matter. Cusco sits at 3,400 m (11,150 ft); Machu Picchu is a full 1,000 m lower at 2,430 m (7,970 ft). The difference affects how you plan the trip.
Most travellers fly into Cusco first, which is the higher point. Altitude symptoms — headache, breathlessness, poor sleep — are more likely on arrival in Cusco than at the citadel itself. Give yourself a day or two in the city (or lower in the Sacred Valley, at Ollantaytambo at 2,790 m) before heading to Machu Picchu. Water, slow pace, coca tea, no alcohol the first night.
By the time you reach Machu Picchu, the lower altitude usually comes as a relief. You can walk the circuits at pace and climb Huayna Picchu or Machu Picchu Mountain without the breathless stops Cusco produces. Still, it’s a hike at 2,430 m — take water, pace the stairs.
Peruways sequences Cusco → Sacred Valley → Machu Picchu in that order for exactly this reason. Have a look at their packages at Peruways.
Short version: Cusco is the hard part. Machu Picchu is where the acclimatisation pays off.
