It was noted as far back as 1700 that 'Chairworkers' seemed tp have an increased risk for several diseases.
Since then, prolonged sitting (as a habit or for work purposes) has been associated with increased risks of developing heart disease, obesity, type 2 diabetes and various cancers.
It's currently not known why long periods of sitting might increase the chances of developing these diseases.
A 2010 review study found that although there are some well established links between sedentary behaviour and disease, they are probably weaker than was prevously thought.
See : Occupational Sitting and Health Risks, A Systematic Review American Journal of Preventive Medicine, Vol. 20, Issue 4.