When Natacyn Isn't Available, You Still Have Options

If your doctor prescribed Natacyn (Natamycin) for a fungal eye infection and you can't find it in stock, you're understandably worried. Fungal eye infections like keratitis need prompt treatment to prevent serious complications, including vision loss.

The good news is that while Natacyn is the only FDA-approved antifungal eye drop, it's not the only antifungal option ophthalmologists use. Several compounded alternatives are widely used in clinical practice.

This article covers what Natacyn is, how it works, and the most common alternatives your doctor may consider if Natacyn is unavailable.

What Is Natacyn?

Natacyn is the brand name for Natamycin 5% ophthalmic suspension, manufactured by Alcon Laboratories. It's a polyene antifungal antibiotic derived from the bacterium Streptomyces natalensis.

Natacyn is FDA-approved for treating:

• Fungal keratitis (corneal infection)
• Fungal conjunctivitis
• Fungal blepharitis (eyelid infection)

It's effective against a range of fungi, including Fusarium, Aspergillus, Candida, Cephalosporium, and Penicillium.

How Does Natacyn Work?

Natacyn belongs to the polyene class of antifungals. It works by binding to ergosterol, a key component of fungal cell membranes. This binding disrupts the membrane's structure, causing the fungal cell to leak essential nutrients and ultimately die.

When applied as eye drops, Natacyn achieves effective concentrations in the corneal stroma (the middle layer of the cornea) but does not penetrate well into the interior of the eye. This makes it ideal for surface-level fungal infections but less effective for deep infections like endophthalmitis.

For more details on how this medication works, see our article: How Does Natacyn Work? Mechanism of Action Explained.

Alternative Antifungal Eye Medications

If Natacyn is unavailable, your ophthalmologist may prescribe one of these alternatives. Important: All of these are compounded formulations — they are not commercially available as ready-made eye drops, so they must be prepared by a compounding pharmacy.

1. Voriconazole 1% Eye Drops (Compounded)

Drug class: Triazole antifungal

Voriconazole is one of the most commonly used alternatives to Natacyn, especially for Aspergillus and Fusarium keratitis. As a triazole antifungal, it works differently from Natacyn — it inhibits an enzyme called lanosterol 14-alpha-demethylase, which fungi need to build their cell membranes.

Key advantages:

• Better penetration into the cornea and aqueous humor than Natacyn
• Effective against many filamentous fungi
• Can also be given orally or intravenously for severe infections

Considerations:

• Must be compounded — not commercially available as eye drops
• May cause temporary burning or stinging on application

2. Amphotericin B 0.15%–0.5% Eye Drops (Compounded)

Drug class: Polyene antifungal

Like Natacyn, Amphotericin B is a polyene antifungal that disrupts the fungal cell membrane. It's been used for decades to treat serious fungal infections and is available as compounded eye drops in concentrations of 0.15% to 0.5%.

Key advantages:

• Broad-spectrum antifungal activity
• Particularly effective against Candida species
• Well-studied with a long track record

Considerations:

• Can cause significant eye irritation and discomfort
• Must be compounded — requires a specialty pharmacy
• Less effective against some filamentous fungi compared to Natacyn

3. Fluconazole 0.2% Eye Drops (Compounded)

Drug class: Triazole antifungal

Fluconazole is another triazole antifungal that can be compounded into eye drops. It's most commonly used for Candida keratitis and is generally well-tolerated.

Key advantages:

• Good penetration into ocular tissues
• Also available as an oral medication for systemic support
• Less irritating than Amphotericin B

Considerations:

• Limited effectiveness against filamentous fungi like Fusarium
• Best suited for yeast infections of the eye
• Must be compounded

How to Get Compounded Antifungal Eye Drops

If your ophthalmologist prescribes a compounded alternative, you'll need a compounding pharmacy that prepares sterile ophthalmic formulations. Not all compounding pharmacies do this — you need one with sterile compounding capabilities.

Steps to follow:

1. Ask your ophthalmologist which compounding pharmacies they work with
2. Contact the compounding pharmacy to confirm they can prepare the medication
3. Confirm turnaround time — some can prepare drops within 24-48 hours
4. Discuss cost upfront, as compounded medications vary widely in price

Should You Wait for Natacyn or Switch to an Alternative?

This is a conversation to have with your ophthalmologist. In general:

• If your infection is caused by Fusarium, Natacyn is often preferred — but Voriconazole is a strong alternative
• If your infection is caused by Candida, Amphotericin B or Fluconazole may work as well or better
• If Natacyn is available nearby, it's usually the first choice because it's FDA-approved and well-studied

Don't delay treatment waiting for Natacyn if an effective alternative is available sooner.

Final Thoughts

Natacyn is the gold standard for treating fungal eye infections, but it's not your only option. If you can't find it:

• Talk to your ophthalmologist about Voriconazole, Amphotericin B, or Fluconazole eye drops
• Find a compounding pharmacy with sterile preparation capabilities
• Use Medfinder to check Natacyn availability while exploring alternatives
• Don't delay treatment — fungal eye infections can cause permanent vision damage if untreated

For the latest on Natacyn availability and pricing, check out our 2026 shortage update.