The glomerular basement membrane is a tissue in the kidney that filters the blood. An abnormal glomerular basement membrane may allow red blood cells into the urinary space. Because kidney stones are so common in people with LPHS, crystals in the kidney tubules may also play a part in bleeding and pain.Other speculations on cause include 
IgA nephropathy. This is a condition in which small amount of a type of normal antibody (called IgA) get stuck in the kidney as it passes through in the bloodstream. This is a chronic condition, which sometimes goes away on its own but occasionally can cause damage to the kidneys. A related condition called IgM nephropathy can sometimes cause pain. Thin membrane disease. In this condition the membrane that filters the blood to make urine is too thin, and blood can pass across it in very small amounts. In a few cases of this condition, there is pain in the kidneys, usually occurring in attacks every so often. Although this condition can be painful, kidney failure does not seem to occur in the long term, so that the only real problem is the symptoms. Infection. In some cases, loin pain-haematuria syndrome occurs after a bladder infection with involvement of the kidney. Even when the infection has been treated and bugs can no longer be found in the urine, pain may persist for 6 months, or even longer in some cases. "Classic loin pain-haematuria syndrome". Some patients have none of the above diagnoses.
Severe renal colic caused by kinking ureter. Pain classically relieved a little by going on all fours with hips higher than head. Diagnosis
LPHS is considered a diagnosis of exclusion. The syndrome presents with hematuria (blood in the urine) and flank (a region of the lower back beneath the ribs and above the ilium) pain which can result from a number of causes. Nonglomerular causes of bleeding (e.g., urinary infection, tumor, or nephrolithiasis) must be excluded. Obstruction of the urinary tract should not be present, confirmed by at least two imaging procedures while pain is present. Diagnosis of loin pain-hematuria syndrome (LPHS) occurs when hematuria is present, recurrent or persistent pain is severe, and other causes of bleeding are excluded. Urine testing can be performed to detect microscopic levels of hematuria. Protein is also commonly found in the urine of patients with LPHS. Kidney biopsies are sometimes performed to look for evidence of glomerular hematuria, excess red blood cells in the kidney tubules, and to assess the width of the glomerular basement membrane. Hematuria (more than 5 red blood cells per high power field) should be present in virtually every urinalysis and is typically characterized by dysmorphic red cells. Recurrent or persistent severe pain for  six months or more, occurring in the costovertebral angles. Relation to chronic pelvic pain
LPHS has considerable overlap with chronic pelvic pain syndrome.