Cusco's high season is June through early September (winter) and the days around the Christmas and Easter holidays. Winter means drier weather and easier traveling, but higher lodging prices and larger crowds. Make reservations for flights to and from Cusco and hotels a few days in advance at this time of year, and weeks in advance if you'll be here for Cusco's famed June 24 Inti Raymi festival, or near Peru's July 28 Independence Day holiday. Prices and visitor numbers drop dramatically during the November through March summer rainy season, except around the holidays. For near-ideal weather and manageable crowds, consider a trip during the spring and autumn months.
The city is compact, so you can visit most sites in a day. However, to fully enjoy Cusco, to have time inside the museums, and to adjust to the high altitude, you need at least two days. The churches close for a few hours in the middle of the day. Get a very early start, or split the walk in two. Most of the city's museums close on Sunday.
All the high-season/low-season trade-offs are found in this region. Winter (June through August) means drier weather and easier traveling, but it's prime vacation time for those in the northern hemisphere. The result is higher lodging prices and larger crowds. Machu Picchu sees up to 3,000 visitors per day during the peak season. The government has not yet set any visitation limits, but conservationists have warned that if the popularity of the sight continues to grow, such limitations are probably in Machu Picchu's best interest. Make reservations for hotels and the Cusco-Machu Picchu train at least few days in advance at this time of year, and weeks in advance if you'll be here for near Peru's July 28 Independence Day holiday. Prices and visitor numbers drop dramatically during the summer rainy season (October through April). For near-ideal weather and manageable crowds, consider a trip in spring or fall.
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