Of the numerous disputes with India and domestic worries,evidently the unsolved problem of Kashmir, his inability to complete the Constitution of the new state of Pakistan, and the plight of the millions of refugees who had arrived in their new homeland utterly destitute affected him the most.
The scale of the refugee problem and the depth of the tragedy were indeed heart rendering. For Pakistan the problem of coping with the refugees was proportionately far more serious than it was for India. Her territory and resources were much smaller and her administration was still in its infancy.
It was not only the plight of the Muslim refugees who had arrived from India that grieved the Quaid-i-Azam deeply. The sad condition of the Hindus in Pakistan hurt him no less.
Apart from Kashmir, there were two Princely states Junagarh and Hyderabad that formed the subject of disputes between India and Pakistan. All the states in the subcontinent except these three had acceded either to India or Pakistan by 14th August 1947. It so happened that all these three were ruled by princes whose own religion was different from that of the majority of their subjects.