In 2019, California accounted for approximately 40% of organic products in the US, and dairy products and milk were the top organic commodity in the state. The objective of this study was to describe organic dairy cattle farmers’ management practices and perceptions of diseases in California. A survey inquiring about farm history and demographics, animal diseases, parasite problems, housing and pasture management, and organic education, was mailed to 160 organic dairy farms, of which 36 (22.5%) responded. Among respondents, the majority (83.9%) were located in Northern California; median farm size was 310 cows, and the dominant breed was Holstein (60.0%). Respondents were more likely to report mastitis in cows (45.2%), pinkeye in heifers (31.3%), and digestive problems in calves (47.0%), as issues affecting their stock “often” or “almost always” in the last 12 months. Although most farmers vaccinated their cattle against Bovine Viral Diarrhea (86.1%) and Escherichia coli mastitis (80.6%), they still described that these diseases frequently impacted their animals. Over half of the farmers did not perceive gastrointestinal parasites or biting flies to be a problem and did not observe signs of lice and mites. According to the results, the management of disease in all age classes is a concern; options and efficacies of alternative therapeutic methods, as well as preventive measures for organic dairies need to be further explored.