Kidney stones are more common in patients with inflammatory bowel disease (IBD) than in the general population. The main lithogenetic risk factors were evaluated in patients affected by Crohn's disease and ulcerative colitis. Our results show the presence of several factors, besides hyperoxaluria, in patients with IBD although their behaviour appears different in Crohn's disease and ulcerative colitis at pre- and post-operative stages. Before surgery in patients with Crohn's disease we found a decreased citrate (p < 0.001) and magnesium (p < 0.005) excretion together with a low urinary volume (p < 0.001) and pH (p < 0.005). After surgery patients with Crohn's disease showed a further reduction of magnesium and citrate. Patients with ulcerative colitis before surgery showed a reduced citrate excretion (p < 0.05) and a more acidic pH (p < 0.05) than healthy subjects. Surgical treatment of proctocolectomy with ileal pouch-anal anastomosis seems to increase the risk of stone formation; in fact, after surgery we observed a relevant decrease of urinary volume (p < 0.001), pH (p < 0.0001) and urinary excretion of citrate (p < 0.0001) as well as magnesium (p < 0.005). Patients with IBD seem to be at greater risk of stone formation than patients with idiopathic calcium lithiasis; in fact, they show a lower excretion of citrate (p < 0.001) and magnesium (p < 0.001) together with a low urinary pH (p < 0.001) and volume (p < 0.001). Urinary volume reduction is probably one of the major risk factors together with the decrease of small molecular weight inhibitors that is a constant finding in all patients with IBD.