Aiims are deemed university, of central importance . they are funded by central government . So the facilities you get there will be of international level as they have to maintain good reputation not only in India but also in the world. Though AIIMS Jodhpur is new(started only in 2012), all the machines, laboratories are new and imported from foreign) . If you join such institute you will get lot of good facilities along with good infrastructure. Moreover you will find a very nice and disciplined culture there, with fully air conditioned hospital. Nevertheless SMS Jaipur is one of the best college and Hospital in Rajasthan , but the AIIMS brand will not only add a tag but will give you more opportunities(foreign) and good exposure to world class equipments.

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Good luck!