Pyelonephritis, a kidney infection, is diagnosed through a combination of symptoms, urine tests, and sometimes blood work or imaging. Most cases can be identified with a focused physical exam and a urinalysis, but confirming the specific bacteria involved requires a urine culture. Imaging is reserved for specific situations where complications are suspected or treatment isn’t working.
Recognizing the Symptoms
The hallmark of pyelonephritis is flank pain paired with a high fever. This combination is what distinguishes a kidney infection from a simple bladder infection, which typically causes only urinary symptoms without fever. The 2025 IDSA guideline update reinforced this distinction, classifying complicated urinary tract infections (including pyelonephritis) based on whether symptoms suggest infection has spread beyond the bladder, with fever being the key indicator.
Beyond flank pain and fever, the full picture often includes:
- Urinary symptoms: burning with urination, frequent urges to go, blood in the urine
- General symptoms: chills, fatigue, feeling generally unwell
- Gastrointestinal symptoms: nausea and vomiting
- Cardiovascular changes: rapid heart rate and blood pressure swings from the systemic infection
In severe cases that are progressing toward sepsis, confusion, rapid breathing, and a significant drop in blood pressure can develop. These are red flags that the infection has entered the bloodstream.
The Physical Exam
During an exam, a clinician will check for costovertebral angle tenderness, which means pain when pressing or lightly tapping over the kidney area on your back, just below the lowest rib. This finding, combined with fever and urinary symptoms, strongly points toward a kidney infection rather than a lower urinary tract infection. Not every patient with pyelonephritis will have obvious tenderness, but when it’s present alongside fever, the diagnosis becomes much more straightforward.
Urine Tests
A urinalysis is the first lab test ordered when pyelonephritis is suspected. The most common finding is pyuria, which means white blood cells are present in the urine, signaling the immune system is actively fighting an infection in the urinary tract. In pregnant patients, pyuria is defined as more than 5 white blood cells per high-power field or a positive leukocyte esterase on a dipstick test, and it has up to 97% sensitivity for urinary tract infections.
Nitrites on a dipstick test are highly specific for bacterial infection (94 to 98%), meaning a positive result is very reliable. However, only about 25% of patients with a urinary tract infection will actually show positive nitrites. This happens because not all bacteria produce the enzyme needed to convert nitrates to nitrites. A negative nitrite result does not rule out pyelonephritis.
A urine culture is the confirmatory test. A clean-catch urine sample is sent to a lab where bacteria are grown and identified. A colony count of 100,000 CFU/mL or more confirms the infection and identifies the exact organism, which guides antibiotic selection. The culture also reveals which antibiotics the bacteria are sensitive or resistant to, which is especially important given rising antibiotic resistance patterns.
Blood Tests
Blood work helps gauge how severe the infection is and whether it has started to affect the rest of the body. A complete blood count will typically show elevated white blood cells. Blood cultures may be drawn if there’s concern the infection has spread to the bloodstream.
Inflammatory markers can help distinguish a kidney infection from a bladder infection when the clinical picture is unclear. A C-reactive protein (CRP) level below 20 mg/L makes pyelonephritis less likely, dropping the probability to under 20%. Procalcitonin, another blood marker, is better suited for confirming pyelonephritis when it’s elevated above 0.5 ng/mL. These markers are particularly useful in children, where symptoms can be vague and localizing an infection to the kidney versus the bladder is harder.
When Imaging Is Needed
Most straightforward cases of pyelonephritis don’t require imaging. A clinical diagnosis based on symptoms, exam findings, and urine results is sufficient for an otherwise healthy person who responds to antibiotics. Imaging becomes important in specific scenarios.
Early imaging is recommended for patients with diabetes, weakened immune systems, a history of kidney stones, or known structural abnormalities of the urinary tract. These patients face higher risks of complications like abscesses, pus buildup in the kidney, or a rare but dangerous form called emphysematous pyelonephritis. A clinical decision rule also flags patients with a urine pH of 7.0 or higher, or significantly reduced kidney function (GFR of 40 mL/min or lower) as needing early imaging.
Imaging is also recommended for anyone who remains feverish or has persistently elevated white blood cell counts after 72 hours of appropriate antibiotic therapy. At that point, the concern shifts to whether there’s an abscess, an obstruction blocking urine flow, or a resistant organism that the antibiotics aren’t covering.
CT Scan Findings
A CT scan with contrast is the most detailed imaging option. Classic findings include swelling of the affected kidney compared to the other side, streaky inflammation in the fat surrounding the kidney (called perinephric stranding), and thickening of the tissue layers around the kidney. A pattern called a striated nephrogram, where the kidney shows alternating bands of higher and lower density, results from blocked tubules and swelling within the kidney tissue. CT is also the best tool for identifying abscesses or gas within the kidney, which signals emphysematous pyelonephritis and requires urgent intervention.
Ultrasound in Pregnancy
For pregnant patients, ultrasound is the preferred imaging method because it avoids radiation. It can identify swelling, fluid collections, or obstructions like kidney stones. If a pregnant patient doesn’t improve within 72 hours of antibiotic therapy, imaging is recommended to rule out other urinary tract problems or complications.
Diagnosis in Children
Diagnosing pyelonephritis in children presents unique challenges because young children can’t always describe their symptoms clearly. Fever without an obvious source in infants and toddlers should always prompt a urine test. Beyond the standard urinalysis and culture, a specialized nuclear medicine scan called a DMSA scan is sometimes used to confirm kidney involvement. In one study, DMSA scintigraphy detected kidney lesions in nearly 79% of children with acute pyelonephritis, making it more sensitive than ultrasound alone for confirming the infection has reached the kidneys.
A voiding cystourethrogram (VCUG), which checks for urine flowing backward from the bladder toward the kidneys, has traditionally been part of the workup. However, research has shown that kidney damage occurs at similar rates whether or not reflux is present, found in about 71 to 72% of kidney units regardless. For children over 5, DMSA scintigraphy may be a more useful investigation than VCUG for evaluating kidney involvement.
Conditions That Mimic Pyelonephritis
Several other conditions can cause flank pain and fever, so part of the diagnostic process involves ruling out alternatives. Kidney stones can cause intense flank pain and sometimes trigger a secondary infection. Appendicitis, particularly when the appendix sits in an unusual position, can mimic right-sided kidney pain. In women, pelvic inflammatory disease can cause lower abdominal and back pain with fever. A kidney abscess or perinephric abscess may look identical to pyelonephritis clinically but requires different management. When urine tests come back negative despite convincing symptoms, these alternatives deserve serious consideration.