Organic Dairy Herd Health: External and Internal Pests and Parasites

eOrganic author:

Linda Tikofsky


Adapted with permission from: Mendenhall, K. (ed.) 2009. The organic dairy handbook: a comprehensive guide for the transition and beyond. Northeast Organic Farming Asociation of New York, Inc., Cobleskill, NY. (Available online at:, verified 18 July 2012).

External Parasites and Diseases of the Skin

Fly Management

Flies are not only a nuisance, they can also impact farm profitability through reduced production and the spread of disease. Biting flies are capable of decreasing milk production by 15% to 30%. Because organic production prohibits synthetic insecticides, organic farmers must take a multi-faceted approach to insect control. Face flies, horn flies, and stable flies are the most common types found in the Northeast (see Table 1).

Table 1. Common flies in the Northeast.
Common Name Location on Animal Problem Level Remarks
Face Fly Face. More than 10 flies per face.
  • Problem when animals are on pasture.
  • Irritation to eyes.
  • Spread of pinkeye.
Horn Fly Back and abdomen. More than 50 flies per side.
  • Problem when animals are on pasture.
  • Rapid life cycle of 10 to 20 days.
  • Female will lay 400 to 500 eggs in her lifetime.
  • Eggs laid in fresh manure.
Stable Fly Legs. More than 10 flies per animal.
  • Problem in barns and on pasture.
  • Rapid life cycle of 14 to 24 days.
  • Female will lay 100 to 400 eggs in her lifetime.
  • Eggs laid in manure and dirt (around feeding areas, drainage areas).

Creating a carefully thought out fly management program and instituting it early in the fly season is essential to success. No single step will control flies; instead, it requires an integrated management plan. The best management practices for fly control are listed in order of priority.

  1. Start control early in the season. Since one female fly can lay 100 to 400 eggs every three weeks, waiting until a problem is noticed may be too late.
  2. Keep pastures and barns clean, dry, and free of manure. Since flies breed in decaying organic material and manure, removing breeding sites will reduce the population of flies. If used for bedding, spread out straw as soon as possible after its removal from stalls. Improve drainage in holding areas and exercise lots. Fence wet or muddy areas out of pastures. Move round bale feeder and scrape areas around feed bunks frequently.
  3. Use pheromone traps and sticky tape in barns to capture adult flies.
  4. Release parasitic wasps. These insects feed on fly larvae and can be released regularly throughout fly season.
  5. Use essential oils and botanicals. These are available from various organic supply companies and can be used as one final step in fly control on your farm. Remember to check with your certifier to be sure that the product is allowed.
  6. Use hydrated lime or diatomaceous earth. These may be used in dust bags to dry the hair coat of cows, making it less attractive to flies.

Ringworm, Lice, and Warts

Ringworm, lice, and warts are diseases of the skin of cattle and are usually contagious. They affect cow comfort and production and are more commonly seen during the winter months when cows spend more time inside (see Table 2).

Table 2. Common causes of common skin diseases and management considerations.
Disease Cause Contributing Factor Signs Management and Treatment
Ringworm Trichophyton verrucosum Immature or compromised immune systems. Circular, grayish crusts especially on eyes, muzzle, and back. Sunlight, fresh air; trace mineral and vitamin supplementation; local treatment with tincture of iodine or tea tree oil.
Lice Sucking or biting of these ectoparasites Crowding, winter months. Decreased production, anemia. Reduce overcrowding; improve nutrition and access to self groomers; hydrated lime or sulfur dust bags; permitted botanical and alternative products.
Warts Papillomavirus Immature immune systems. Warts on head, neck, and teats, injury to skin. Time; vaccination.


Infectious bovine keratoconjunctivitis (IBK or pinkeye) is caused by the bacteria Moraxella bovis. Conditions that irritate the eye and surrounding structures (including flies, plant material and stubble, dust, and viruses) allow infection by the bacteria. Initial signs of the disease include tearing, redness, swelling, and sensitivity to light (squinting). As the disease advances, a cloudy area may appear on the surface of the eye that gradually spreads. The eye may bulge or eventually rupture. Conventional farms usually inject antibiotics into the conjunctiva of the eye. However, organic management does NOT allow this and must rely on good fly control and prevention of irritation to the eye.

Follow good grazing practices to prevent stubble from injuring eye tissues. Consider vaccinating before fly season. Make sure nutrition is adequate. For extremely irritated eyes, place an eye patch or have your veterinarian temporarily sew the third eyelid over the globe to speed healing and lessen the pain.

Alternative Therapy for Pinkeye

The following therapies may not be scientifically evaluated or appropriate for all farms. Make sure you consult the References and Citations section at the end of this article for specific instructions.

  • Calendula eyewash sprayed in affected eye twice daily.

Internal Parasites of Cattle

Animals on pasture are at higher risk for infestation by internal parasites. In your organic systems plan (OSP), develop grazing management strategies to minimize potential infection and transfer among age groups on your farm.


The most common intestinal worms affecting cattle in the Northeast are the brown stomach worm (Ostertagia ostertagi), the barber pole worm (Haemonchus contortus), and Cooperia spp. Larvae overwinter in cattle in the Northeast and begin to mature and produce eggs in the springtime, shedding in cattle feces. Figure 1 illustrates the nematode lifecycle.

Figure 1. Nematode lifecycle. Credit: Mendenhall, K. (ed.) 2009. The organic dairy handbook: a comprehensive guide for the transition and beyond. Northeast Organic Farming Asociation of New York, Inc., Cobleskill, NY.

Worm infestation may be clinical (visible signs) or subclinical. Clinical infections are more common in young cattle and calves. They may have diarrhea, poor weight gain, potbellies, rough and discolored hair coats, or swelling under the jaw (bottle jaw). In subclinical infestations (most common in adult cattle), diarrhea rarely occurs but the worms negatively affect milk production and body condition. Many adult cattle develop some level of immunity to intestinal parasites.

Organic farmers manage nematodes through best management practices and alternative therapies. The National Organic Program (NOP) allows synthetic dewormers (only Ffenbendazole, Ivermectin, and Moxidectin) only on an emergency basis in organic dairy cattle not designated as organic slaughter stock. Routine dewormers cannot be used. Instead, the organic system plan (OSP) must include a management plan to reduce youngstock exposure to parasites. These management steps are included in the article, "Pasture Management on Organic Dairy Farms: Pasture Pitfalls."

Alternative Therapies for Nematodes

The following therapies may not be scientifically evaluated or appropriate for all farms. Make sure you consult the References and Citations section at the end of this article for specific instructions.

  • Black walnut hulls and/or wormwood.
  • Garlic.


Bovine coccidiosis is caused by Eimeria spp., tiny, one-celled organisms. Most of the negative effects of coccidiosis occur in young animals (calves and heifers) and infestations are characterized by diarrhea (often with blood), weight loss, anemia, and dehydration. Death is usually due to dehydration or secondary bacterial infections.

Coccidia have a complex lifecycle. Oocysts (eggs) are shed in feces. These oocysts are quite hardy and can survive for months in moist areas, particularly where sunlight and ventilation is minimal. They are unaffected by common disinfectants. The oocysts change life stage in the environment and are then ingested by calves. Inside the calf intestine, the oocysts release sporozoites that burrow into the intestinal wall. Inside the intestinal wall, they undergo a few more life stages and eventually release more oocysts into the feces and into the environment. One ingested oocyst ultimately results in 20 million additional oocysts shed into the environment.

The severity of symptoms directly relates to the number of oocysts ingested; so, the more contaminated or less hygienic an area, the greater the risk of oocyst exposure. Overcrowding, stress, diet changes, or shipping can cause an outbreak. Follow the same best management practices used to prevent scours. The three currently NOP-approved synthetic dewormers are NOT effective for coccidiosis.

Also in This Series

This article is part of a series discussing organic dairy herd health. For more information, see the following articles.

References and Citations

Additional Resources


Published February 7, 2013

This is an eOrganic article and was reviewed for compliance with National Organic Program regulations by members of the eOrganic community. Always check with your organic certification agency before adopting new practices or using new materials. For more information, refer to eOrganic's articles on organic certification.