Sorry this is long. Hope it doesn't cause undue worry. At this point the vet option is probably your best bet, but it sounds like this could be a sign of something more serious.
Conjunctivitis and
Corneal Disease in Cats
"The Squinting Cat"
Cats don't have as many eye problems as dogs do, but when an eye disease occurs in a cat, it is usually chronic, lasting months to years, and sometimes is a lifetime problem for the cat. Conjunctivitis is inflammation of the pink membrane part of the eye, which lines the white part (sclera) and the inner eyelid. The conjunctiva can become quite reddened and swollen in some cats, and often it is just in one eye and not in both. This causes intermittent or constant squinting. It can occur on and off, for months to years. The conjunctivitis may occur without any other eye problems, or the eye may also have a corneal ulcer or erosion (painful open sore on the cornea, which is the "clear windshield" part of the eye), Keratitis (corneal inflammation), and/or uveitis (intraocular inflammation). Corneal involvement and uveitis are often caused by Feline Herpesvirus-1 (see discussion below).
Signs of conjunctivitis:
Signs include squinting (which is severe if the cornea has an ulcer or erosion) and mucoid or watery discharge (that can be clear, gray, yellow, green, or a rusty dark red color that looks like dried blood but ISN'T). Cats that have this unusual dark tear color are often Persians or Himalayans. The conjunctiva is reddened and sometimes swollen or thickened. The cornea can be clear, or can be cloudy if there is an ulcer, erosion, or scar tissue present. The iris (the colored part of the inside of the eye, that forms the pupil) can be a different color too (usually a "muddier", duller color than normal), if uveitis is present. All of these eye signs may be present, or some of them, and it may be in both eyes or one eye. Sometimes the cat shows signs of an upper respiratory tract infection (URTI), and is sneezing.
Causes of conjunctivitis:
Most of the causes are infectious. While many different kinds of infectious organisms can cause conjunctivitis, there are only three that are common culprits: Feline Herpesvirus-1 (FHV-1), Feline Chlamydia, and Feline Mycoplasma. It is important to know that a case of conjunctivitis can have one, two, or all three organisms together causing the problem, and that Feline Herpesvirus cannot be transmitted to people -- only to cats. It is a very species-specific virus.
Diagnosing the cause of conjunctivitis and/or keratitis:
Often, the medical history and the clinical signs present are sufficient to aid in diagnosis, but sometimes special tests are needed. These tests include (but are not limited to): collection of conjunctival and/or corneal cells for culture, or cytology (looking at the cells under a microscope), or special DNA tests for FHV-1 infection.
Treatment of conjunctivitis and keratitis:
Corneal erosion (stained with diagnostic flourescein dye) in a cat, caused by FHV-1.
Mycoplasmal infections usually respond well to topical antibiotics, and Chlamydial infections often also respond, but can recur. However, FHV-1 infections do not respond at all to topical antibiotic therapy, and are very frustrating to treat. Sometimes topical antiviral medications are also used.
Because FHV-1 conjunctivitis and keratitis are complicated diseases, we will discuss this virus in more detail:
FHV-1 is a very common virus in cats, and most of the cats on this planet have it, and are exposed to it when they are small kittens. The virus can then be dormant in the cat's body for the rest of the cat's life, or flare up and cause problems at any time. A key factor in the severity of the disease and how recurrent it is, is STRESS. Anything that stresses the cat can suppress the immune system and allow the virus to reactivate and cause problems. This is similar to coldsores in people, which is caused by a human herpesvirus. Cold sores can worsen when the person is stressed. Cats are the same way!
It is also important to know that FHV-1 conjunctivitis and/or keratitis cannot be cured, only controlled. In between flare-ups, the cat's eyes can be quite normal. Flare-ups can occur frequently, or there can be years in between each flare-up. Some cats will never have a flare-up.
There are many different possible treatments for conjunctivitis caused by FHV-1, depending on the clinical signs present, and there are even more different drug treatment choices if the cornea is involved. If the cornea is involved, vision might be compromised if the virus is not controlled, but it is rare for a cat with ocular FHV-1 infection to become totally blinded by the disease. Rather, the disease is more likely to cause long-term pain and discomfort without proper treatment.
What to do if you suspect conjunctivitis and/or keratitis in your cat:
First of all, have your family veterinarian examine your pet. Sometimes your doctor may recommend referral to a veterinary ophthalmologist (which is often the case if FHV-1 is suspected to be present) if your cat's eyes are not improving with medication or are worsening.

Conjunctivitis and
Corneal Disease in Cats
"The Squinting Cat"
Cats don't have as many eye problems as dogs do, but when an eye disease occurs in a cat, it is usually chronic, lasting months to years, and sometimes is a lifetime problem for the cat. Conjunctivitis is inflammation of the pink membrane part of the eye, which lines the white part (sclera) and the inner eyelid. The conjunctiva can become quite reddened and swollen in some cats, and often it is just in one eye and not in both. This causes intermittent or constant squinting. It can occur on and off, for months to years. The conjunctivitis may occur without any other eye problems, or the eye may also have a corneal ulcer or erosion (painful open sore on the cornea, which is the "clear windshield" part of the eye), Keratitis (corneal inflammation), and/or uveitis (intraocular inflammation). Corneal involvement and uveitis are often caused by Feline Herpesvirus-1 (see discussion below).
Signs of conjunctivitis:
Signs include squinting (which is severe if the cornea has an ulcer or erosion) and mucoid or watery discharge (that can be clear, gray, yellow, green, or a rusty dark red color that looks like dried blood but ISN'T). Cats that have this unusual dark tear color are often Persians or Himalayans. The conjunctiva is reddened and sometimes swollen or thickened. The cornea can be clear, or can be cloudy if there is an ulcer, erosion, or scar tissue present. The iris (the colored part of the inside of the eye, that forms the pupil) can be a different color too (usually a "muddier", duller color than normal), if uveitis is present. All of these eye signs may be present, or some of them, and it may be in both eyes or one eye. Sometimes the cat shows signs of an upper respiratory tract infection (URTI), and is sneezing.
Causes of conjunctivitis:
Most of the causes are infectious. While many different kinds of infectious organisms can cause conjunctivitis, there are only three that are common culprits: Feline Herpesvirus-1 (FHV-1), Feline Chlamydia, and Feline Mycoplasma. It is important to know that a case of conjunctivitis can have one, two, or all three organisms together causing the problem, and that Feline Herpesvirus cannot be transmitted to people -- only to cats. It is a very species-specific virus.
Diagnosing the cause of conjunctivitis and/or keratitis:
Often, the medical history and the clinical signs present are sufficient to aid in diagnosis, but sometimes special tests are needed. These tests include (but are not limited to): collection of conjunctival and/or corneal cells for culture, or cytology (looking at the cells under a microscope), or special DNA tests for FHV-1 infection.
Treatment of conjunctivitis and keratitis:
Corneal erosion (stained with diagnostic flourescein dye) in a cat, caused by FHV-1.
Mycoplasmal infections usually respond well to topical antibiotics, and Chlamydial infections often also respond, but can recur. However, FHV-1 infections do not respond at all to topical antibiotic therapy, and are very frustrating to treat. Sometimes topical antiviral medications are also used.
Because FHV-1 conjunctivitis and keratitis are complicated diseases, we will discuss this virus in more detail:
FHV-1 is a very common virus in cats, and most of the cats on this planet have it, and are exposed to it when they are small kittens. The virus can then be dormant in the cat's body for the rest of the cat's life, or flare up and cause problems at any time. A key factor in the severity of the disease and how recurrent it is, is STRESS. Anything that stresses the cat can suppress the immune system and allow the virus to reactivate and cause problems. This is similar to coldsores in people, which is caused by a human herpesvirus. Cold sores can worsen when the person is stressed. Cats are the same way!
It is also important to know that FHV-1 conjunctivitis and/or keratitis cannot be cured, only controlled. In between flare-ups, the cat's eyes can be quite normal. Flare-ups can occur frequently, or there can be years in between each flare-up. Some cats will never have a flare-up.
There are many different possible treatments for conjunctivitis caused by FHV-1, depending on the clinical signs present, and there are even more different drug treatment choices if the cornea is involved. If the cornea is involved, vision might be compromised if the virus is not controlled, but it is rare for a cat with ocular FHV-1 infection to become totally blinded by the disease. Rather, the disease is more likely to cause long-term pain and discomfort without proper treatment.
What to do if you suspect conjunctivitis and/or keratitis in your cat:
First of all, have your family veterinarian examine your pet. Sometimes your doctor may recommend referral to a veterinary ophthalmologist (which is often the case if FHV-1 is suspected to be present) if your cat's eyes are not improving with medication or are worsening.