Jordan Taylor
September 29, 2026
The ICD-10-CM code for vitamin D deficiency is E55.9, Vitamin D deficiency, unspecified. It covers low vitamin D, hypovitaminosis D, vitamin D insufficiency, and vitamin D3 deficiency in adults and children, whenever the provider diagnoses the deficiency and it isn't active rickets. It's billable, and it has no severity subcodes.
The diagnosis code is simple. What trips up claims is the test around it. A vitamin D level ordered as a screen is coded Z13.21, not E55.9, and Medicare doesn't pay for vitamin D screening at all. Coverage for CPT 82306 depends on the diagnosis on the order and on your Medicare contractor's local policy. This guide covers the codes, the screening rules, the lab CPT codes, and what keeps these claims from denying.
E55.9 sits in Chapter 4, endocrine, nutritional and metabolic diseases, under category E55. The category header E55 isn't billable. The Alphabetic Index sends avitaminosis D and calciferol deficiency here, and in practice low vitamin D, hypovitaminosis D, vitamin D insufficiency, and D3 deficiency all land on the same code. There's no separate code for mild, severe, or chronic deficiency.
Category E55 carries an Excludes1 note. These conditions are coded to their own codes, not E55:
• Adult osteomalacia, M83.-
• Osteoporosis with current pathological fracture, M80.-
• Sequelae of rickets, E64.3
That osteoporosis exclusion is narrower than it looks. It lists M80, osteoporosis with a current fracture. Age-related osteoporosis without a fracture, M81.0, isn't on the list, so a patient with both vitamin D deficiency and osteoporosis can have E55.9 and M81.0 reported together when both are documented and addressed.
The same vitamin D test can carry four different diagnosis codes depending on why it was ordered and what's already known about the patient.
Screening, Z13.21. A patient with no symptoms and no known deficiency gets a vitamin D level as part of a routine workup. That's a screen, and the correct code is Z13.21, encounter for screening for nutritional disorder. E55.9 can't be used to justify a test ordered before any deficiency was found. If the screen comes back low and the provider diagnoses a deficiency, E55.9 goes on the next encounter.
Diagnosed deficiency, E55.9. Once the provider documents vitamin D deficiency or insufficiency, E55.9 applies. It stays the right code during replacement therapy, because the patient is still being treated for the condition, and that's what supports follow-up levels.
Symptoms or risk factor, not screening. A test ordered because of fatigue, bone pain, a fall, or a condition that affects vitamin D (such as chronic kidney disease or gastric bypass) is diagnostic, not a screen. Code the symptom or condition that prompted it.
History, Z86.39. When the deficiency has resolved and the patient is no longer on treatment, it's history, Z86.39. A patient still taking a prescribed replacement dose isn't history yet.
Elevated vitamin D. High vitamin D the provider diagnoses as hypervitaminosis D is E67.3. When it comes from taking too much of a supplement, the vitamin T code is added: T45.2X1A for an accidental excess, or T45.2X5A for an adverse effect at a prescribed dose. A high result the provider doesn't address isn't coded.
Rickets. Active rickets in a child from vitamin D deficiency is E55.0, which replaces E55.9. Past rickets with lasting effects is E64.3. Vitamin D-resistant rickets isn't a vitamin D deficiency at all; it's a phosphate disorder, coded E83.31, familial hypophosphatemia.
Osteomalacia. Adult osteomalacia is excluded from category E55, so it's coded from M83 instead. When the provider ties it to malnutrition or poor intake, that's M83.3, adult osteomalacia due to malnutrition; other specified forms use M83.8.
Osteoporosis. As noted above, E55.9 can sit alongside M81.0 for osteoporosis without a current fracture. With a current fragility fracture, the M80 code applies and E55 is excluded.
Pregnancy. A vitamin D deficiency that the provider documents as complicating a pregnancy is coded with O99.28-, endocrine, nutritional and metabolic diseases complicating pregnancy, with the trimester character (O99.281, O99.282, O99.283, or O99.280 if unspecified), followed by E55.9 and a Z3A code for weeks of gestation. If the provider documents the deficiency as incidental to the pregnancy, E55.9 is reported with Z33.1 instead.
Underlying causes. When a condition is driving the deficiency and the provider documents it, that condition is coded as well, since it often decides whether the lab test is covered: chronic kidney disease (N18.3- through N18.6), bariatric surgery status (Z98.84), intestinal malabsorption (K90.9), obesity (E66.-), and long-term use of glucocorticoids (Z79.52).
82306 is the test almost every vitamin D order means. Lab catalog names vary, such as "Vitamin D, 25-OH, Total, IA" or "25-hydroxy vitamin D2 and D3," but they bill as 82306, and "includes fractions" means the D2 and D3 breakdown isn't billed separately. Ordering 82652 as a routine deficiency check is a common source of denials, since it doesn't measure body stores.
Medicare doesn't cover vitamin D testing for routine screening. That limit comes from the rule that Medicare pays for diagnostic tests ordered to manage a specific problem, and CMS has made vitamin D testing an approved Recovery Audit topic because so many claims don't meet it.
Coverage is set by each Medicare Administrative Contractor's local coverage determination, such as L34658 (WPS), L36692 (Noridian, JE), and L34051 (Noridian, JF). They broadly cover testing for conditions that affect vitamin D or that vitamin D affects, including chronic kidney disease stage 3 or higher, osteoporosis and osteopenia, osteomalacia, rickets, hypocalcemia and hypercalcemia, parathyroid disorders, malabsorption, gastric bypass, liver disease, obesity, long-term use of drugs that lower vitamin D, and monitoring a known deficiency during treatment. Each LCD's billing article lists the exact diagnosis codes, and frequency limits differ by contractor; some limit testing to once a year for most indications but allow more for known deficiency and rickets.
When a Medicare patient wants a screen anyway, give the patient an Advance Beneficiary Notice before the draw and append modifier GA to 82306, so the patient can be billed if Medicare denies it. Without a signed ABN, the practice or lab absorbs the cost.
Commercial and Medicaid plans vary. Many follow the same logic as Medicare and deny screening for low-risk adults, while others cover a set number of tests a year with an approved diagnosis. Check the plan's lab policy before assuming coverage.
• The reason for the test, in words: screening, a symptom, a risk condition, or monitoring a known deficiency
• The level and the reference range, once available, and the provider's interpretation (deficient, insufficient, normal)
• The diagnosis in the assessment: vitamin D deficiency, not just "low D" in the lab table
• Treatment: dose, form, and duration
• The follow-up plan: when the next level is due and why
• Any underlying condition that explains the deficiency
The order and the claim need to match. A test ordered with Z13.21 and then billed with E55.9, with no deficiency documented before the draw, is the kind of mismatch audits look for.
Most of these start at ordering, so the fix is upstream: matching the diagnosis on the requisition to the reason documented in the note. A regular medical billing audit of lab claims shows quickly whether vitamin D tests are going out under the wrong code, a pre-submission medical coding check catches the Excludes1 and screening errors, and denial management sorts out which denials can be appealed and which need an ABN process instead.
• CMS, ICD-10-CM official code files and guidelines, current code set
• CMS, LCD L34658, Vitamin D Assay Testing
• CMS, Approved RAC Topic 0143: Vitamin D Assay Testing
E55.9, vitamin D deficiency, unspecified. It's billable and covers every severity.
E55.9 as well, once the provider diagnoses it. There's no separate insufficiency code.
Z13.21, encounter for screening for nutritional disorder. Medicare doesn't cover vitamin D screening.
Z86.39, personal history of other endocrine, nutritional and metabolic disease, once the deficiency has resolved and treatment has stopped.
E67.3, hypervitaminosis D, when the provider diagnoses it, with a T45.2 code if a supplement caused it.
Vitamin deficiency, unspecified, for a vitamin deficiency where the vitamin isn't named. Vitamin D deficiency always uses E55.9.
82306, vitamin D; 25 hydroxy. 82652 is the 1,25 dihydroxy test, used only for specific indications.
Those listed in your MAC's vitamin D LCD billing article, such as chronic kidney disease stage 3 or higher, osteoporosis, osteomalacia, hypocalcemia, malabsorption, gastric bypass, and known vitamin D deficiency being treated. Routine screening isn't covered.
O99.28- with the trimester, then E55.9 and a Z3A code, when the provider documents it as complicating the pregnancy.
E83.31, familial hypophosphatemia.
Explore more medical billing guides, coding updates, and revenue cycle tips.
R53.1 is the ICD-10 code for weakness. Learn when to use M62.81, R54, R53.81, or R53.83 instead, and why R53.1...
R74.01 is the ICD-10 code for transaminitis and elevated ALT or AST. Learn R74.01 vs R74.8 and R94.5, drug-ind...
Every abdominal pain ICD-10 code in the R10 family, from R10.9 and R10.84 to the new flank, suprapubic and mul...
